JP2004109053A - Binding part prediction method and apparatus, program, and recording medium - Google Patents

Abstract

<P>PROBLEM TO BE SOLVED: To provide a system etc. for predicting three-dimensional structure information from information on the amino acids of proteins and predicting electrostatically unstable parts from the three-dimensional structure information and electric charge. <P>SOLUTION: In the system, distance data in a space between amino acid residues in the three-dimensional structure of the proteins or bioactive polypeptides is determined from data on the amino acid sequence of the proteins or the bioactive polypeptides (step SA-1), and binding parts are predicted by specifying electrostatically undatable amino acid residues according to the distance data and the electric charge of each amino acid (sep SA-2 to 4). Therefore, it is possible to highly accurately predict the binding parts at a high speed by using that amino acid residues which could become electrostatically unstable easily become binding parts from the amino acid sequence of the proteins or the bioactive polypeptides. <P>COPYRIGHT: (C)2004,JPO

Description

【０１３５】
また、図１８は本発明により求めたアセチルコリン・エステラーゼ・インヒビターのエネルギーを示す図である。図１８からアセチルコリン・エステラーゼ・インヒビターのエネルギーが０以上のもの１０個を結合部位候補として取り出し、実際に結合部位かどうかを実験的に調べると、その内に７個は実際に結合部位であった（図１９）。
【０１３６】
以上のように極めて高精度に結合部位を予測することができる。実施例２では既知の立体構造情報を利用した点が実施例１とは異なる点である。つまり、実施例１と実施例２では空間距離の決定手法を変えているが、いずれも良好な結果を与えたことから、どのような空間距離の決定手法を使っても、本発明の効果が期待できると考えられる。
これにて、本発明の実施例２が終了する。
【０１３７】
［本発明の実施例３；「ｈｕｎｔｉｎｇｔｉｎ−ａｓｓｏｃｉｔａｔｅｄ　ｐｒｏｔｅｉｎ　ｉｎｔｅｒａｃｔｉｎｇ　ｐｒｏｔｅｉｎ」と、「ｎｉｔｒｉｃ　ｏｘｉｄｅ　ｓｙｎｔｈａｓｅ　２Ａ」との複合体］
次に、本発明の実施例３の詳細について図２０等を参照して説明する。実施例３は２つの蛋白質が結合する時の結合部位予測に関する。「ｈｕｎｔｉｎｇｔｉｎ−ａｓｓｏｃｉｔａｔｅｄ　ｐｒｏｔｅｉｎ　ｉｎｔｅｒａｃｔｉｎｇ　ｐｒｏｔｅｉｎ」は、「ｎｉｔｒｉｃ　ｏｘｉｄｅ　ｓｙｎｔｈａｓｅ　２Ａ」と結合することが実験的に分かっている。更に、結合部位は「ｈｕｎｔｉｎｇｔｉｎ−ａｓｓｏｃｉｔａｔｅｄ　ｐｒｏｔｅｉｎ　ｉｎｔｅｒａｃｔｉｎｇ　ｐｒｏｔｅｉｎ」はアミノ酸残基番号６００付近であり、「ｎｉｔｒｉｃ　ｏｘｉｄｅｓｙｎｔｈａｓｅ　２Ａ」はアミノ酸残基番号１００付近であることが分かっている。
【０１３８】
ここで、本実施例においても実施例１と同様にして配列情報の獲得、立体構造の予測、電荷の決定を行った。ただし、アミノ酸間の配列上の距離から空間的な距離に変換する方法は、蛋白質がガウス鎖をとると仮定し、配列上の距離と空間上の距離とを以下の式で関係づけた。
ｒ＝３．８　ｄ^０．５
ここでｒは空間上の距離、ｄは配列上の距離である。
【０１３９】
また、複合体構造生成は上述した高速計算手法を使った。つまり、次式を用いた。
（空間上の距離）＝　ｋ（｜Ａ上の着目残基と結合残基の配列上の距離｜＋｜Ｂ上の着目残基と結合残基の配列上の距離｜）　^ｎ
【０１４０】
そして、それぞれの結合部位を仮定した複合体のエネルギーを計算し、図２０を作成することができた。ここで、図２０は横軸に、ｈｕｎｔｉｎｇｔｉｎ−ａｓｓｏｃｉｔａｔｅｄ　ｐｒｏｔｅｉｎ　ｉｎｔｅｒａｃｔｉｎｇ　ｐｒｏｔｅｉｎの結合部位のアミノ酸残基番号をとり、縦軸にｎｉｔｒｉｃ　ｏｘｉｄｅ　ｓｙｎｔｈａｓｅ　２Ａの結合部位のアミノ酸残基番号をとり、各結合部位で複合体を生成したときのエネルギーの総和を等高線表示したものである。
【０１４１】
図２０によれば、例えば、ｈｕｎｔｉｎｇｔｉｎ−ａｓｓｏｃｉｔａｔｅｄ　ｐｒｏｔｅｉｎ　ｉｎｔｅｒａｃｔｉｎｇ　ｐｒｏｔｅｉｎのアミノ酸残基５００番と、ｎｉｔｒｉｃ　ｏｘｉｄｅ　ｓｙｎｔｈａｓｅ　２Ａのアミノ酸残基１５０番とが結合部位の場合の複合体のエネルギーは−１０というように、結合部位ごとのエネルギーが求められる。
【０１４２】
図２０に示すように、エネルギーの極小部は２つあり、１つはｈｕｎｔｉｎｇｔｉｎ−ａｓｓｏｃｉｔａｔｅｄ　ｐｒｏｔｅｉｎ　ｉｎｔｅｒａｃｔｉｎｇ　ｐｒｏｔｅｉｎの結合部位がアミノ酸残基６００〜９５０付近で、ｎｉｔｒｉｃｏｘｉｄｅ　ｓｙｎｔｈａｓｅ　２Ａの結合部位がアミノ酸残基２５〜１００付近で結合した場合であり、もう１つはｈｕｎｔｉｎｇｔｉｎ−ａｓｓｏｃｉｔａｔｅｄ　ｐｒｏｔｅｉｎ　ｉｎｔｅｒａｃｔｉｎｇ　ｐｒｏｔｅｉｎの結合部位がアミノ酸残基６５０〜９００付近で、ｎｉｔｒｉｃ　ｏｘｉｄｅ　ｓｙｎｔｈａｓｅ　２Ａの結合部位がアミノ酸残基４７５〜５００付近で結合した場合である。
【０１４３】
ここで、前者が実際の結合部位に対応している（図中の黒丸で囲んだ部分）。以上のように、２つの蛋白質の結合部位を正確に予測することができた。
これにて、本発明の実施例３が終了する。
【０１４４】
［本発明の実施例４；Ｅ２Ｆ　ｔｒａｎｓｃｒｉｐｔｉｏｎ　ｆａｃｔｏｒ　１］次に、本発明の実施例４の詳細について図２１等を参照して説明する。
実施例４は結合相手予測に関する。Ｅ２Ｆ　ｔｒａｎｓｃｒｉｐｔｉｏｎ　ｆａｃｔｏｒ　１（以下、Ｅ２Ｆ１）は相互作用相手に関する情報が実験的に良く調べられている蛋白質である。
【０１４５】
ここで、Ｅ２Ｆ１と相互作用する相手をＨｏｍｏ　Ｓａｐｉｅｎｓの遺伝子のデータベース（ここでは無作為に６６００個を抽出した）から探し、候補蛋白質のアミノ酸配列データとした。
【０１４６】
そして、実施例３で計算した手順と同様に、相手の候補蛋白質ごとにＥ２Ｆ１との結合部位を探す。そして、最もエネルギーが安定（最小）になった時のエネルギーを相互作用エネルギーとする。図２１は各候補蛋白質の相互作用エネルギーと遺伝子の数のヒストグラムである。
【０１４７】
図２１に示したように、相対的な相互作用エネルギーを計算することができた。例えば、相互作用エネルギーが９０よりも大きい（エネルギーが−９０よりも小さい）ものは１００個あるが、ここにあるものが相互作用相手である可能性が高い。この方法は非常に高速で、相互作用を網羅的に計算することができる。
これにて、本発明の実施例４が終了する。
【０１４８】
［他の実施の形態］
さて、これまで本発明の実施の形態について説明したが、本発明は、上述した実施の形態以外にも、上記特許請求の範囲に記載した技術的思想の範囲内において種々の異なる実施の形態にて実施されてよいものである。
【０１４９】
例えば、結合部位予測装置１００がスタンドアローンの形態で処理を行う場合を一例に説明したが、結合部位予測装置１００とは別筐体で構成されるクライアント端末からの要求に応じて処理を行い、その処理結果を当該クライアント端末に返却するように構成してもよい。
【０１５０】
また、実施形態において説明した各処理のうち、自動的に行なわれるものとして説明した処理の全部または一部を手動的に行うこともでき、あるいは、手動的に行なわれるものとして説明した処理の全部または一部を公知の方法で自動的に行うこともできる。
この他、上記文書中や図面中で示した処理手順、制御手順、具体的名称、各種の登録データや検索条件等のパラメータを含む情報、画面例、データベース構成については、特記する場合を除いて任意に変更することができる。
【０１５１】
また、結合部位予測装置１００に関して、図示の各構成要素は機能概念的なものであり、必ずしも物理的に図示の如く構成されていることを要しない。
例えば、結合部位予測装置１００の各部または各装置が備える処理機能、特に制御部１０２にて行なわれる各処理機能については、その全部または任意の一部を、ＣＰＵ（Ｃｅｎｔｒａｌ　Ｐｒｏｃｅｓｓｉｎｇ　Ｕｎｉｔ）および当該ＣＰＵにて解釈実行されるプログラムにて実現することができ、あるいは、ワイヤードロジックによるハードウェアとして実現することも可能である。なお、プログラムは、後述する記録媒体に記録されており、必要に応じて結合部位予測装置１００に機械的に読み取られる。
【０１５２】
すなわち、ＲＯＭまたはＨＤなどの記憶部１０６などには、ＯＳ（Ｏｐｅｒａｔｉｎｇ　Ｓｙｓｔｅｍ）と協働してＣＰＵに命令を与え、各種処理を行うためのコンピュータプログラムが記録されている。このコンピュータプログラムは、ＲＡＭ等にロードされることによって実行され、ＣＰＵと協働して制御部１０２を構成する。また、このコンピュータプログラムは、結合部位予測装置１００に対して任意のネットワーク３００を介して接続されたアプリケーションプログラムサーバに記録されてもよく、必要に応じてその全部または一部をダウンロードすることも可能である。
【０１５３】
また、本発明にかかるプログラムを、コンピュータ読み取り可能な記録媒体に格納することもできる。ここで、この「記録媒体」とは、フレキシブルディスク、光磁気ディスク、ＲＯＭ、ＥＰＲＯＭ、ＥＥＰＲＯＭ、ＣＤ−ＲＯＭ、ＭＯ、ＤＶＤ等の任意の「可搬用の物理媒体」や、各種コンピュータシステムに内蔵されるＲＯＭ、ＲＡＭ、ＨＤ等の任意の「固定用の物理媒体」、あるいは、ＬＡＮ、ＷＡＮ、インターネットに代表されるネットワークを介してプログラムを送信する場合の通信回線や搬送波のように、短期にプログラムを保持する「通信媒体」を含むものとする。
【０１５４】
また、「プログラム」とは、任意の言語や記述方法にて記述されたデータ処理方法であり、ソースコードやバイナリコード等の形式を問わない。なお、「プログラム」は必ずしも単一的に構成されるものに限られず、複数のモジュールやライブラリとして分散構成されるものや、ＯＳ（Ｏｐｅｒａｔｉｎｇ　Ｓｙｓｔｅｍ）に代表される別個のプログラムと協働してその機能を達成するものをも含む。なお、実施の形態に示した各装置において記録媒体を読み取るための具体的な構成、読み取り手順、あるいは、読み取り後のインストール手順等については、周知の構成や手順を用いることができる。
【０１５５】
記憶部１０６に格納される各種のデータベース等（アミノ酸配列データベース１０６ａ〜処理結果ファイル１０６ｇ）は、ＲＡＭ、ＲＯＭ等のメモリ装置、ハードディスク等の固定ディスク装置、フレキシブルディスク、光ディスク等のストレージ手段であり、各種処理やウェブサイト提供に用いる各種のプログラムやテーブルやファイルやデータベースやウェブページ用ファイル等を格納する。
【０１５６】
また、結合部位予測装置１００は、既知のパーソナルコンピュータ、ワークステーション等の情報処理端末等の情報処理装置にプリンタやモニタやイメージスキャナ等の周辺装置を接続し、該情報処理装置に本発明の方法を実現させるソフトウェア（プログラム、データ等を含む）を実装することにより実現してもよい。
【０１５７】
さらに、結合部位予測装置１００の分散・統合の具体的形態は図示のものに限られず、その全部または一部を、各種の負荷等に応じた任意の単位で、機能的または物理的に分散・統合して構成することができる。例えば、各データベースを独立したデータベース装置として独立に構成してもよく、また、処理の一部をＣＧＩ（Ｃｏｍｍｏｎ　Ｇａｔｅｗａｙ　Ｉｎｔｅｒｆａｃｅ）を用いて実現してもよい。
【０１５８】
また、ネットワーク３００は、結合部位予測装置１００と外部システム２００とを相互に接続する機能を有し、例えば、インターネットや、イントラネットや、ＬＡＮ（有線／無線の双方を含む）や、ＶＡＮや、パソコン通信網や、公衆電話網（アナログ／デジタルの双方を含む）や、専用回線網（アナログ／デジタルの双方を含む）や、ＣＡＴＶ網や、ＩＭＴ２０００方式、ＧＳＭ方式またはＰＤＣ／ＰＤＣ―Ｐ方式等の携帯回線交換網／携帯パケット交換網や、無線呼出網や、Ｂｌｕｅｔｏｏｔｈ等の局所無線網や、ＰＨＳ網や、ＣＳ、ＢＳまたはＩＳＤＢ等の衛星通信網等のうちいずれかを含んでもよい。すなわち、本システムは、有線・無線を問わず任意のネットワークを介して、各種データを送受信することができる。
【０１５９】
【発明の効果】
以上詳細に説明したように、本発明によれば、蛋白質または生理活性ポリペプチドのアミノ酸配列データから当該蛋白質または生理活性ポリペプチドの立体構造における各アミノ酸残基間の空間上の距離データを求め、当該距離データと各アミノ酸の電荷に従って静電的に不安定なアミノ酸残基を特定することにより結合部位を予測するので、蛋白質または生理活性ポリペプチドのアミノ酸配列から静電的に不安定になりそうなアミノ酸残基が結合部位になりやすいことを利用して、高速かつ高精度に結合部位を予測することができる結合部位予測方法、結合部位予測装置、プログラム、および、記録媒体を提供することができる。
【０１６０】
また、本発明によれば、目的の蛋白質または生理活性ポリペプチドのアミノ酸配列データを取得し、取得されたアミノ酸配列データに含まれる各アミノ酸残基の間の空間上の距離を決定し、アミノ酸配列データに含まれる各アミノ酸残基が持つ電荷を決定し、決定された各アミノ酸残基間の空間上の距離と、決定された各アミノ酸残基が持つ電荷とに従って、各アミノ酸残基のエネルギーを計算し、計算されたエネルギーに従って、結合部位となる候補アミノ酸残基を決定するので、蛋白質または生理活性ポリペプチドのアミノ酸配列から静電的に不安定になりそうなアミノ酸残基が結合部位になりやすいことを利用して、高速かつ高精度に結合部位を予測することができる結合部位予測方法、結合部位予測装置、プログラム、および、記録媒体を提供することができる。
【０１６１】
また、本発明によれば、目的の複数の蛋白質または生理活性ポリペプチドのアミノ酸配列データを取得し、目的の複数の蛋白質または生理活性ポリペプチドの結合した複合体の立体構造情報を生成し、取得された複数のアミノ酸配列データに含まれる各アミノ酸残基の間の空間上の距離を、生成した複合体の立体構造情報に従って決定し、複数のアミノ酸配列データに含まれる各アミノ酸残基が持つ電荷を決定し、決定された各アミノ酸残基間の空間上の距離と、決定された各アミノ酸残基が持つ電荷とに従って、各アミノ酸残基のエネルギーを計算し、複合体について結合部位を変えて複合体の立体構造情報を生成し、各アミノ酸残基のエネルギーを計算し、当該エネルギーの総和が最小となる結合部位を求め、エネルギーの総和が最小となる結合部位を、結合部位の候補アミノ酸残基として決定するので、蛋白質または生理活性ポリペプチドのアミノ酸配列から静電的に不安定になりそうなアミノ酸残基が結合部位になりやすいことを利用して、高速かつ高精度に結合部位を予測することができる結合部位予測方法、結合部位予測装置、プログラム、および、記録媒体を提供することができる。
【０１６２】
さらに、本発明によれば、目的の蛋白質または生理活性ポリペプチドのアミノ酸配列データと、結合候補となる１つまたは複数の蛋白質または生理活性ポリペプチドのアミノ酸配列データとを取得し、目的の蛋白質または生理活性ポリペプチドと、結合候補となる蛋白質または生理活性ポリペプチドとが結合した複合体の立体構造情報を生成し、取得された目的のアミノ酸配列データと結合候補のアミノ酸配列データに含まれる各アミノ酸残基の間の空間上の距離を、生成した複合体の立体構造情報に従って決定し、目的のアミノ酸配列データと結合候補のアミノ酸配列データに含まれる各アミノ酸残基が持つ電荷を決定し、決定された各アミノ酸残基間の空間上の距離と、決定された各アミノ酸残基が持つ電荷とに従って、各アミノ酸残基のエネルギーを計算し、複合体について結合部位を変えて複合体の立体構造情報を生成し、各アミノ酸残基のエネルギーを計算し、当該エネルギーの総和が最小となる結合部位を求め、全ての結合候補についてエネルギー最小化処理を実行した結果、エネルギーの総和が最小となる結合部位をもつ結合候補を決定するので、蛋白質または生理活性ポリペプチドのアミノ酸配列から静電的に不安定になりそうなアミノ酸残基が結合部位になりやすいことを利用して、高速かつ高精度に最適な結合候補の蛋白質を予測することができる結合部位予測方法、結合部位予測装置、プログラム、および、記録媒体を提供することができる。
【図面の簡単な説明】
【図１】本発明により１つの蛋白質のアミノ酸配列情報からその蛋白質の結合部位を予測する場合の概念を説明する図である。
【図２】本発明により複数の蛋白質のアミノ酸配列情報からそれらの蛋白質で複合体を形成するときの結合部位を予測する場合の概念を説明する図である。
【図３】本発明が適用される本システムの構成の一例を示すブロック図である。
【図４】本発明が適用される空間距離決定部１０２ｂの構成の一例を示すブロック図である。
【図５】本発明が適用されるエネルギー計算部１０２ｄの構成の一例を示すブロック図である。
【図６】本発明の高速計算手法の概念を示す図である。
【図７】複数のアミノ酸配列上で結合残基を仮定する場合の概念を示す図である。
【図８】着目残基の概念を説明する図である。
【図９】本実施形態における本システムの処理の一例を示すフローチャートである。
【図１０】処理結果の候補アミノ酸残基のエネルギーなどの一例を示す図である。
【図１１】立体構造上で不安定な部分がクラスター化している場合の一例を示す図である。
【図１２】ドッキングシミュレーションを用いて複合体構造を生成する場合の概念を示す図である。
【図１３】蛋白質Ａと蛋白質Ｂの各アミノ酸残基を結合残基とした場合のエネルギーの総和をプロットした図の一例である。
【図１４】２つのグルタミン酸の配列上の距離と空間上の距離との関係を示す図である。
【図１５】リボヌクレアーゼＡの各アミノ酸残基のエネルギーをアミノ酸残基番号に対してプロットした図である。
【図１６】リボヌクレアーゼＡのアミノ酸残基のエネルギーが０以上のものを結合部位候補として表にまとめた図である。
【図１７】ＰＤＢに格納されたアセチルコリン・エステラーゼ・インヒビターの立体構造情報データの一部を示す図である。
【図１８】本発明により求めたアセチルコリン・エステラーゼ・インヒビターのエネルギーを示す図である。
【図１９】アセチルコリン・エステラーゼ・インヒビターのエネルギーが０以上のもの１０個を結合部位候補として取り出し、実際に結合部位かどうかを実験的に調べた結果を示す図である。
【図２０】横軸に、ｈｕｎｔｉｎｇｔｉｎ−ａｓｓｏｃｉｔａｔｅｄ　ｐｒｏｔｅｉｎ　ｉｎｔｅｒａｃｔｉｎｇ　ｐｒｏｔｅｉｎの結合部位のアミノ酸残基番号をとり、縦軸にｎｉｔｒｉｃ　ｏｘｉｄｅ　ｓｙｎｔｈａｓｅ　２Ａの結合部位のアミノ酸残基番号をとり、各結合部位で複合体を生成したときのエネルギーの総和を等高線表示した図である。
【図２１】各候補蛋白質の相互作用エネルギーと遺伝子の数のヒストグラムである。
【符号の説明】
１００　結合部位予測装置
１０２　制御部
１０２ａ　アミノ酸配列データ取得部
１０２ｂ　空間距離決定部
１０２ｃ　電荷決定部
１０２ｄ　エネルギー計算部
１０２ｅ　候補アミノ酸残基決定部
１０２ｆ　複合体構造生成部
１０２ｇ　エネルギー最小化部
１０２ｈ　結合候補データ取得部
１０２ｉ　結合部位予測部
１０２ｊ　結合相手候補決定部
１０２ｋ　高速計算部
１０２ｍ　構造データ利用計算部
１０２ｎ　シミュレーションデータ利用計算部
１０２ｐ　全エネルギー計算部
１０２ｑ　相互作用エネルギー計算部
１０４　通信制御インターフェース部
１０６　記憶部
１０６ａ　アミノ酸配列データベース
１０６ｂ　蛋白質構造データベース
１０６ｃ　距離データファイル
１０６ｄ　全エネルギーデータファイル
１０６ｅ　相互作用エネルギーデータファイル
１０６ｆ　複合体構造データファイル
１０６ｇ　処理結果ファイル
１０８　入出力制御インターフェース部
１１２　入力装置
１１４　出力装置
２００　外部システム
３００　ネットワーク[0001]
TECHNICAL FIELD OF THE INVENTION
The present invention relates to a binding site prediction method, a binding site prediction device, a program, and a recording medium, and particularly to three-dimensional structure information (space between amino acid residues) predicted from amino acid sequence data or experimentally determined. By predicting an electrostatically unstable portion using the above distance information and charge information, it is possible to efficiently predict a binding site or a binding partner of a protein or a bioactive polypeptide, and the like. The present invention relates to a binding site prediction method, a binding site prediction device, a program, and a recording medium.
[0002]
[Prior art]
In order for a protein or a physiologically active polypeptide to exhibit a certain function, it is important that it interacts with another protein or the like. Substances that inhibit or enhance the interaction of certain proteins have the potential to become pharmaceuticals. Therefore, predicting the interaction site of a protein and the interaction partner of the protein is a very important problem in biology, medicine, and pharmacy. For this reason, in the field of bioinformatics, it has been conventionally attempted to predict a protein interacting partner by various methods.
[0003]
[Problems to be solved by the invention]
However, known methods for predicting protein interactions using bioinformatics are computationally intensive and require a long processing time. Also, since the prediction accuracy is low, it is desired to develop a method with higher accuracy and shorter processing time. Had the problem of being rare.
Hereinafter, the content of this problem will be described more specifically.
[0004]
For example, with respect to the interaction site prediction in the field of bioinformatics, a prediction technique by motif search or the like has been developed. However, the motif search has a problem that it can analyze a known interaction site, but cannot analyze an unknown interaction site.
[0005]
In addition, a method for predicting a binding site using amino acid frequency analysis has been developed. For example, there are Patent Literature 1, Patent Literature 2, Patent Literature 3, and the like. However, these prediction methods have a problem that prediction accuracy is low.
[0006]
[Patent Document 1]
JP-A-11-213003
[Patent Document 2]
JP-A-10-222486
[Patent Document 3]
JP-A-10-045795
[0007]
In addition, for example, there is a method of docking the three-dimensional structures of two proteins to obtain the most stable complex structure. Although the prediction accuracy of this method is high, there are some problems. First, most proteins do not have a known three-dimensional structure, so they cannot be applied to most proteins. Second, these methods have a large computational load and require a long processing time, so that it is difficult to perform an exhaustive calculation.
[0008]
In addition, no effective means has been established for the interaction partner prediction, which is more difficult than the interaction site prediction. In other words, a completely new approach is required to predict a completely unknown interaction site and further an interaction partner with high accuracy, but an effective means has not yet been established.
[0009]
SUMMARY OF THE INVENTION The present invention has been made in view of the above problems, and a binding site prediction method and a binding site prediction device that enable prediction of protein interaction by bioinformatics in a very short time and enable comprehensive analysis. , A program, and a recording medium.
[0010]
[Means for Solving the Problems]
In order for two proteins to interact spontaneously, binding requires that the energy of the entire system be reduced. That is, an unstable portion in a protein has a possibility of being stabilized by binding, and thus can be considered as a portion that is easily bound. In addition, it is considered that the interaction partner has a higher binding ability than other proteins. In other words, in order to predict an interaction partner, it is necessary to exhaustively calculate an interaction and then search for one having a higher ability to interact than others. To do so, it is necessary to calculate not only one-to-one interactions but also many-to-many interactions, so that it is necessary to greatly reduce the calculation cost.
[0011]
The central concept of the present invention is that a region that is more unstable than other sites in the structure of a protein is more likely to be a binding site. That is, the present invention predicts a binding site by obtaining a locally unstable region by relatively simple calculation.
[0012]
That is, the present invention mainly comprises
-Basically, it should be possible to predict the binding site with high accuracy from only the protein sequence information (however, three-dimensional structure information can be added if necessary).
-It is characterized by the two points that calculation can be performed in a very short time and comprehensive analysis can be performed.
[0013]
The present invention has been made in view of the above-mentioned problems, and predicts three-dimensional structure information (space distance between amino acids) from amino acid information of a protein, and is electrostatically unstable from three-dimensional structure and charge information. Binding site prediction method and / or binding site prediction, which can predict a binding site and / or a binding partner by predicting a proper part and / or calculating electrostatic energy when two proteins bind. The present invention relates to an apparatus, a program, and a recording medium.
[0014]
In order to achieve such an object, the method for predicting a binding site according to claim 1 uses the space between each amino acid residue in the three-dimensional structure of the protein or the biologically active polypeptide from the amino acid sequence data of the protein or the biologically active polypeptide. The above distance data is obtained, and the binding site is predicted by specifying an electrostatically unstable amino acid residue according to the distance data and the charge of each amino acid.
[0015]
According to this method, spatial distance data between each amino acid residue in the three-dimensional structure of the protein or the biologically active polypeptide is obtained from the amino acid sequence data of the protein or the biologically active polypeptide, and the distance data and the charge of each amino acid are determined. The binding site is predicted by specifying an electrostatically unstable amino acid residue according to the formula, so that an amino acid residue that is likely to be electrostatically unstable from the amino acid sequence of the protein or the bioactive polypeptide is added to the binding site. Utilizing the fact that the binding site is likely to be used, the binding site can be quickly and accurately predicted.
[0016]
Further, the method for predicting a binding site according to claim 2 includes the steps of: obtaining an amino acid sequence data for obtaining an amino acid sequence data of a target protein or a physiologically active polypeptide; and obtaining the amino acid sequence data obtained by the amino acid sequence data obtaining step. A spatial distance determining step of determining a spatial distance between each amino acid residue included, a charge determining step of determining the charge of each amino acid residue included in the amino acid sequence data, and the spatial distance determining step An energy calculating step of calculating the energy of each amino acid residue according to the determined spatial distance between each amino acid residue and the charge of each amino acid residue determined in the charge determining step; Candidate binding site according to the energy calculated in step Characterized in that it comprises a candidate amino acid residue determining step of determining a amino acid residues.
[0017]
According to this method, the amino acid sequence data of the target protein or the biologically active polypeptide is obtained, the spatial distance between each amino acid residue contained in the obtained amino acid sequence data is determined, and the amino acid sequence data is obtained. The charge of each amino acid residue included is determined, and the energy of each amino acid residue is calculated according to the determined spatial distance between each amino acid residue and the determined charge of each amino acid residue. Since the candidate amino acid residue serving as the binding site is determined according to the calculated energy, the amino acid residue which is likely to be electrostatically unstable from the amino acid sequence of the protein or the biologically active polypeptide is likely to become the binding site. , It is possible to predict a binding site at high speed and with high accuracy.
[0018]
In addition, the binding site prediction method according to claim 3 includes an amino acid sequence data obtaining step of obtaining amino acid sequence data of a plurality of target proteins or biologically active polypeptides; The complex structure generation step of generating the three-dimensional structure information of the bound complex, and the spatial distance between each amino acid residue included in the plurality of amino acid sequence data obtained in the amino acid sequence data obtaining step, A spatial distance determining step for determining according to the three-dimensional structure information of the complex generated by the complex structure generating step; a charge determining step for determining a charge of each amino acid residue included in the plurality of amino acid sequence data; The spatial distance between each amino acid residue determined in the distance determining step and the charge determination An energy calculation step of calculating the energy of each amino acid residue according to the charge of each amino acid residue determined by TEP, and a binding site of the complex by changing the binding site in the complex in the complex structure generation step Generates structural information, calculates the energy of each amino acid residue by an energy calculation step, and calculates an energy minimization step for finding a binding site where the sum of the energy is minimized. Determining the candidate binding site as a candidate amino acid residue of the binding site.
[0019]
According to this method, amino acid sequence data of a plurality of target proteins or bioactive polypeptides is obtained, and three-dimensional structure information of a complex in which the plurality of target proteins or bioactive polypeptides is bound is obtained. The spatial distance between each amino acid residue contained in the plurality of amino acid sequence data is determined according to the three-dimensional structure information of the generated complex, and the charge of each amino acid residue contained in the plurality of amino acid sequence data is determined. Then, the energy of each amino acid residue is calculated according to the determined spatial distance between each amino acid residue and the determined charge of each amino acid residue, and the binding site of the complex is changed to change the complex. , Calculate the energy of each amino acid residue, find the binding site that minimizes the sum of the energies, and minimize the sum of the energies Since the binding site is determined as a candidate amino acid residue of the binding site, the amino acid residue which is likely to be electrostatically unstable from the amino acid sequence of the protein or the biologically active polypeptide is likely to become the binding site. Thus, the binding site can be predicted at high speed and with high accuracy.
[0020]
The method for predicting a binding site according to claim 4 obtains amino acid sequence data of a protein or a biologically active polypeptide of interest and amino acid sequence data of one or more proteins or biologically active polypeptides as binding candidates. An amino acid sequence data obtaining step, and a complex structure generating step of generating three-dimensional structure information of a complex in which the target protein or bioactive polypeptide and the protein or bioactive polypeptide as the binding candidate are bound, The complex generated in the complex structure generating step is a spatial distance between the target amino acid sequence data obtained in the amino acid sequence data obtaining step and each amino acid residue included in the amino acid sequence data of the binding candidate. A spatial distance determination step determined according to the three-dimensional structure information of A charge determination step of determining the charge of each amino acid residue contained in the sequence data and the amino acid sequence data of the binding candidate, a spatial distance between each amino acid residue determined by the spatial distance determination step, An energy calculating step for calculating the energy of each amino acid residue according to the charge of each amino acid residue determined in the charge determining step; and a complex site by changing a binding site of the complex by the complex structure generating step. And the energy minimizing step of calculating the energy of each amino acid residue by an energy calculating step, and finding a binding site where the sum of the energies is minimized, and the energy minimizing step for all the binding candidates As a result, the binding site where the sum of the above energies is minimized One characterized in that it comprises a binding candidate determining step of determining a binding candidate.
[0021]
According to this method, the amino acid sequence data of the target protein or biologically active polypeptide and the amino acid sequence data of one or more proteins or biologically active polypeptides as binding candidates are obtained, and the target protein or biologically active polypeptide is obtained. The polypeptide and a protein or a bioactive polypeptide as a binding candidate generate steric structure information of a complex bound thereto, and the obtained target amino acid sequence data and each amino acid residue included in the binding candidate amino acid sequence data Was determined according to the three-dimensional structure information of the generated complex, and the charge of each amino acid residue contained in the target amino acid sequence data and the amino acid sequence data of the binding candidate was determined. The energy of each amino acid residue is determined according to the spatial distance between each amino acid residue and the determined charge of each amino acid residue. Energy, calculate the steric structure information of the complex by changing the binding site for the complex, calculate the energy of each amino acid residue, find the binding site that minimizes the sum of the energies, and calculate all binding candidates As a result of performing the energy minimizing process on the amino acid sequence, a binding candidate having a binding site that minimizes the total energy is determined. Therefore, amino acid residues that are likely to be electrostatically unstable from the amino acid sequence of the protein or the biologically active polypeptide are determined. By taking advantage of the fact that the group is likely to be a binding site, it becomes possible to predict an optimal binding candidate protein at high speed and with high accuracy.
[0022]
Further, the present invention relates to a binding site prediction device, wherein the binding site prediction device according to claim 5 comprises an amino acid sequence data acquisition means for acquiring amino acid sequence data of a target protein or a physiologically active polypeptide; A spatial distance determining means for determining a spatial distance between each amino acid residue contained in the amino acid sequence data obtained by the sequence data obtaining means; and a charge possessed by each amino acid residue contained in the amino acid sequence data. Charge determining means, the spatial distance between each amino acid residue determined by the spatial distance determining means, and the charge of each amino acid residue determined by the charge determining means, Energy calculating means for calculating energy; and a coupling unit according to the energy calculated by the energy calculating means. Characterized by comprising a candidate amino acid residue determining means for determining a candidate amino acid residue to be.
[0023]
According to this device, the amino acid sequence data of the target protein or the biologically active polypeptide is obtained, the spatial distance between each amino acid residue contained in the obtained amino acid sequence data is determined, and the amino acid sequence data is obtained. The charge of each amino acid residue included is determined, and the energy of each amino acid residue is calculated according to the determined spatial distance between each amino acid residue and the determined charge of each amino acid residue. Since the candidate amino acid residue serving as the binding site is determined according to the calculated energy, the amino acid residue which is likely to be electrostatically unstable from the amino acid sequence of the protein or the biologically active polypeptide is likely to become the binding site. , It is possible to predict a binding site at high speed and with high accuracy.
[0024]
Further, the binding site predicting apparatus according to claim 6 comprises an amino acid sequence data acquiring means for acquiring amino acid sequence data of a plurality of target proteins or biologically active polypeptides, and a plurality of target proteins or biologically active polypeptides. The complex structure generating means for generating the three-dimensional structure information of the bound complex, and the spatial distance between each amino acid residue included in the plurality of amino acid sequence data obtained by the amino acid sequence data obtaining means, A spatial distance determining means for determining in accordance with the three-dimensional structure information of the complex generated by the complex structure generating means, a charge determining means for determining a charge of each amino acid residue contained in the plurality of amino acid sequence data, The spatial distance between each amino acid residue determined by the distance determining means and each amino acid determined by the charge determining means According to the charge of the residue, energy calculating means for calculating the energy of each amino acid residue, and the complex structure generating means to generate a three-dimensional structure information of the complex by changing the binding site for the complex, Calculating the energy of each amino acid residue by the calculating means, calculating an energy minimizing means for determining a binding site at which the sum of the energy is minimized; and And means for determining a candidate amino acid residue.
[0025]
According to this apparatus, amino acid sequence data of a plurality of target proteins or bioactive polypeptides is obtained, and three-dimensional structure information of a complex in which the plurality of target proteins or bioactive polypeptides is bound is generated. The spatial distance between each amino acid residue contained in the plurality of amino acid sequence data is determined according to the three-dimensional structure information of the generated complex, and the charge of each amino acid residue contained in the plurality of amino acid sequence data is determined. Then, the energy of each amino acid residue is calculated according to the determined spatial distance between each amino acid residue and the determined charge of each amino acid residue, and the binding site of the complex is changed to change the complex. , Calculate the energy of each amino acid residue, find the binding site that minimizes the sum of the energies, and minimize the sum of the energies Since the binding site is determined as a candidate amino acid residue of the binding site, the amino acid residue which is likely to be electrostatically unstable from the amino acid sequence of the protein or the biologically active polypeptide is likely to become the binding site. Thus, the binding site can be predicted at high speed and with high accuracy.
[0026]
Further, the binding site predicting apparatus according to claim 7 obtains amino acid sequence data of a target protein or a biologically active polypeptide and amino acid sequence data of one or more proteins or biologically active polypeptides as binding candidates. An amino acid sequence data obtaining means, and a complex structure generating means for generating three-dimensional structure information of a complex in which the target protein or bioactive polypeptide and the binding candidate protein or bioactive polypeptide are bound, The complex produced by the complex structure producing means is a spatial distance between the target amino acid sequence data acquired by the amino acid sequence data acquiring means and each amino acid residue contained in the amino acid sequence data of the binding candidate. Spatial distance determining means for determining in accordance with the three-dimensional structure information of the target; Charge determination means for determining the charge of each amino acid residue contained in the amino acid sequence data of the candidate, the spatial distance between each amino acid residue determined by the spatial distance determination means, and determined by the charge determination means Energy calculating means for calculating the energy of each amino acid residue according to the charge of each amino acid residue, and the complex structure generating means for changing the binding site of the complex to obtain the three-dimensional structure information of the complex. Generated, the energy of each amino acid residue is calculated by the energy calculation means, the energy minimization means for finding the binding site where the sum of the energy is minimized, and the result of executing the energy minimization means for all the binding candidates, Binding candidate determining means for determining a binding candidate having a binding site that minimizes the sum of the energies And it features.
[0027]
According to this device, the amino acid sequence data of the target protein or biologically active polypeptide and the amino acid sequence data of one or more proteins or biologically active polypeptides as binding candidates are obtained, and the target protein or biologically active polypeptide is obtained. The polypeptide and a protein or a bioactive polypeptide as a binding candidate generate steric structure information of a complex bound thereto, and the obtained target amino acid sequence data and each amino acid residue included in the binding candidate amino acid sequence data Was determined according to the three-dimensional structure information of the generated complex, and the charge of each amino acid residue contained in the target amino acid sequence data and the amino acid sequence data of the binding candidate was determined. The energy of each amino acid residue is determined according to the spatial distance between each amino acid residue and the determined charge of each amino acid residue. Energy, calculate the steric structure information of the complex by changing the binding site for the complex, calculate the energy of each amino acid residue, find the binding site that minimizes the sum of the energies, and calculate all binding candidates As a result of performing the energy minimizing process on the amino acid sequence, a binding candidate having a binding site that minimizes the total energy is determined. Therefore, amino acid residues that are likely to be electrostatically unstable from the amino acid sequence of the protein or the biologically active polypeptide are determined. By taking advantage of the fact that the group is likely to be a binding site, it becomes possible to predict an optimal binding candidate protein at high speed and with high accuracy.
[0028]
The present invention also relates to a program, wherein the program according to claim 8 is obtained by an amino acid sequence data obtaining step of obtaining an amino acid sequence data of a target protein or a physiologically active polypeptide, and the amino acid sequence data obtaining step. A spatial distance determining step of determining a spatial distance between each amino acid residue included in the amino acid sequence data, and a charge determining step of determining the charge of each amino acid residue included in the amino acid sequence data, Energy calculation for calculating the energy of each amino acid residue according to the spatial distance between each amino acid residue determined in the spatial distance determination step and the charge of each amino acid residue determined in the charge determination step And the energy calculated by the energy calculating step. Over accordingly, characterized in that to perform the binding site prediction method including the candidate amino acid residue determining step of determining a candidate amino acid residue to be the binding site to the computer.
[0029]
According to this program, the amino acid sequence data of the target protein or the biologically active polypeptide is obtained, the spatial distance between each amino acid residue included in the obtained amino acid sequence data is determined, and the amino acid sequence data is obtained. The charge of each amino acid residue included is determined, and the energy of each amino acid residue is calculated according to the determined spatial distance between each amino acid residue and the determined charge of each amino acid residue. Since the candidate amino acid residue serving as the binding site is determined according to the calculated energy, the amino acid residue which is likely to be electrostatically unstable from the amino acid sequence of the protein or the biologically active polypeptide is likely to become the binding site. , It is possible to predict a binding site at high speed and with high accuracy.
[0030]
Further, the program according to the ninth aspect of the present invention is a program wherein an amino acid sequence data obtaining step of obtaining amino acid sequence data of a plurality of target proteins or biologically active polypeptides is combined with the plurality of target proteins or biologically active polypeptides. A complex structure generating step of generating three-dimensional structural information of the body, and a spatial distance between each amino acid residue included in the plurality of amino acid sequence data obtained in the amino acid sequence data obtaining step, A spatial distance determining step for determining in accordance with the three-dimensional structure information of the complex generated in the generating step; a charge determining step for determining a charge of each amino acid residue included in the plurality of amino acid sequence data; and the spatial distance determining step The spatial distance between each amino acid residue determined by The energy calculation step of calculating the energy of each amino acid residue according to the charge of each amino acid residue determined by the above, and the three-dimensional structure of the complex by changing the binding site for the complex by the complex structure generating step Generates information, calculates the energy of each amino acid residue by an energy calculation step, and minimizes the energy by the energy minimization step of finding a binding site where the sum of the energy is minimized, and minimizes the energy by the energy minimization step Determining a binding site as a candidate amino acid residue of the binding site by a computer.
[0031]
According to this program, amino acid sequence data of a plurality of target proteins or bioactive polypeptides is obtained, and three-dimensional structure information of a complex in which the plurality of target proteins or bioactive polypeptides is bound is obtained. The spatial distance between each amino acid residue contained in the plurality of amino acid sequence data is determined according to the three-dimensional structure information of the generated complex, and the charge of each amino acid residue contained in the plurality of amino acid sequence data is determined. Then, the energy of each amino acid residue is calculated according to the determined spatial distance between each amino acid residue and the determined charge of each amino acid residue, and the binding site of the complex is changed to change the complex. The three-dimensional structure information is generated, the energy of each amino acid residue is calculated, the binding site where the sum of the energies is minimized is determined, and the sum of the energies is minimized. Is determined as a candidate amino acid residue for the binding site, and the fact that amino acid residues that are likely to be electrostatically unstable from the amino acid sequence of a protein or a biologically active polypeptide tend to become the binding site is used. Thus, the binding site can be predicted with high speed and high accuracy.
[0032]
Further, the program according to claim 10 is an amino acid sequence for obtaining amino acid sequence data of a target protein or biologically active polypeptide and amino acid sequence data of one or more proteins or biologically active polypeptides that are binding candidates. A data acquisition step, a complex structure generating step of generating three-dimensional structure information of a complex in which the target protein or bioactive polypeptide and the binding candidate protein or bioactive polypeptide are bound, and the amino acid sequence The spatial distance between the target amino acid sequence data obtained in the data obtaining step and each amino acid residue contained in the amino acid sequence data of the binding candidate is determined by the three-dimensional structure of the complex generated in the complex structure generating step. Determining a spatial distance determined according to the information; A charge determining step for determining the charge of each amino acid residue contained in the data and the amino acid sequence data of the binding candidate; a spatial distance between each amino acid residue determined by the spatial distance determining step; According to the charge of each amino acid residue determined in the determining step, an energy calculating step of calculating the energy of each amino acid residue, and changing the binding site of the complex by the complex structure generating step, Generate three-dimensional structure information, calculate the energy of each amino acid residue by an energy calculation step, and perform an energy minimization step of finding a binding site where the sum of the energies is minimized, and the energy minimization step of all the binding candidates. As a result of execution, there is a binding site that minimizes the sum of the above energies Possible to execute the binding site prediction method and a binding candidate determination step of determining if a candidate to the computer and said.
[0033]
According to this program, amino acid sequence data of a target protein or biologically active polypeptide and amino acid sequence data of one or more proteins or biologically active polypeptides as binding candidates are obtained, and the target protein or biologically active polypeptide is obtained. The polypeptide and a protein or a bioactive polypeptide as a binding candidate generate steric structure information of a complex bound thereto, and the obtained target amino acid sequence data and each amino acid residue included in the binding candidate amino acid sequence data Was determined according to the three-dimensional structure information of the generated complex, and the charge of each amino acid residue contained in the target amino acid sequence data and the amino acid sequence data of the binding candidate was determined. Each amino acid residue is determined according to the spatial distance between each amino acid residue and the determined charge of each amino acid residue. Calculate the energy, change the binding site for the complex, generate steric structure information of the complex, calculate the energy of each amino acid residue, find the binding site that minimizes the sum of the energies, and determine all binding candidates As a result of performing the energy minimizing process on the amino acid sequence, a binding candidate having a binding site that minimizes the total energy is determined. Therefore, amino acid residues that are likely to be electrostatically unstable from the amino acid sequence of the protein or the biologically active polypeptide are determined. By taking advantage of the fact that the group is likely to be a binding site, it becomes possible to predict an optimal binding candidate protein at high speed and with high accuracy.
[0034]
Further, the present invention relates to a recording medium, wherein a recording medium according to claim 11 records the program according to any one of claims 8 to 10.
[0035]
According to this recording medium, a program recorded in the recording medium is read by a computer and executed, thereby realizing the program described in any one of claims 8 to 10 using a computer. And the same effect as each of these methods can be obtained.
[0036]
BEST MODE FOR CARRYING OUT THE INVENTION
Hereinafter, embodiments of a binding site prediction method, a binding site prediction device, a program, and a recording medium according to the present invention will be described in detail with reference to the drawings. The present invention is not limited by the embodiment.
In particular, in the following embodiments, an example in which the present invention is applied to an amino acid sequence of a protein or the like will be described. However, the present invention is not limited to this, and is similarly applied to a case where an amino acid sequence of a bioactive polypeptide is used. can do.
[0037]
[Summary of the present invention]
Hereinafter, the outline of the present invention will be described, and then the configuration, processing, and the like of the present invention will be described in detail. 1 and 2 are principle configuration diagrams showing the basic principle of the present invention. The present invention generally has the following basic features.
[0038]
FIG. 1 is a diagram illustrating the concept of predicting the binding site of a protein from the amino acid sequence information of the protein according to the present invention.
As shown in FIG. 1, first, in the present invention, spatial distance data between each amino acid residue in the three-dimensional structure of a protein is determined from amino acid sequence data of a protein or a physiologically active polypeptide (step SA-1).
[0039]
Here, for example, the following three methods are available for obtaining distance data in space.
[0040]
1) High-speed calculation method
This method is a method of converting a distance on the sequence between amino acids into a spatial distance. FIG. 6 is a diagram showing the concept of the high-speed calculation method of the present invention. Assuming that the three-dimensional structure of the protein takes a Gaussian chain, the distance in the amino acid sequence of the protein and the distance in space in the three-dimensional structure of the protein can be related by the following formula.
r = k dⁿ(0 <n <1)
Here, r is a distance in space, d is a distance in the array, and k is a proportional constant. That is, if the distance d on the array is known, the distance r on the space can be calculated. The values of k and n are obtained by statistically processing the relationship between the sequence distance and the spatial distance between amino acids from three-dimensional structural information collected in a protein structure database such as PDB (Protein Data Bank). Then, an appropriate value may be set. Here, n is 0 to 1, but preferably 0.5 to 0.6. Also, k is in the range of 2.8 to 4.8, preferably in the range of 3.3 to 4.3. This method is a very powerful method when processing a large amount of protein, for example, when handling tens of thousands of proteins, because the algorithm is very simple and the calculation load is very small.
[0041]
2) Calculation method using structural data
This method is a method of accurately obtaining the actual spatial distance between amino acid residues by using the three-dimensional structure information data registered in the protein structure database. For example, when the three-dimensional structure information data of the target protein is stored in a protein structure database such as a PDB, by obtaining the three-dimensional structure information data registered in the database, the distance in space can be accurately calculated as follows. Can be calculated.
[0042]
For example, the spatial distance R between amino acid residue number I and amino acid residue number J_IJRepresents coordinates (x) of the amino acid residue number I such as the center of gravity or a specific main chain atom._I, Y_I, Z_I), And coordinates such as the center of gravity of amino acid residue number J and atoms of a specific main chain are (x_J, Y_J, Z_J) Can be calculated as follows.
R_IJ ²= (X_I-X_J)²+ (Y_I-Y_J)²+ (Z_I-Z_J)²
(Where R_IJ> 0)
[0043]
3) Calculation method using simulation data
In this method, a protein whose structure is unknown is subjected to a protein structure simulation by a known structure simulation method, and a spatial distance is obtained using the simulation data (expected three-dimensional structure information data). There are various methods for three-dimensional structure prediction simulation, such as homology modeling. For example, it is introduced in detail in "Practical Bioinformatics" (C. Gibas, P. Jambeck, O'Reilly Japan 2002).
[0044]
This method has a drawback that the calculation load is large as compared with the method 1 and the method 2, but has an advantage that an almost accurate spatial distance can be obtained for a protein having an unknown structure.
[0045]
A feature of the present invention is that a plurality of calculation methods are made possible in each step. In particular, in order to compensate for the drawback that the three-dimensional structure prediction method using the existing simulation method is time-consuming, a method of simply determining spatial distance data between amino acid residues from amino acid sequence data as in Method 1 is combined. This enables a high-speed calculation and a prediction method for processing a large amount of data, such as prediction of a coupling partner.
[0046]
Next, the present invention calculates the total energy of the protein according to the distance data and the charge of each amino acid (step SA-2).
[0047]
Here, various methods for determining the charge of the amino acid can be considered. For example, the charge of a positively charged charged amino acid (lysine, arginine) is 1, the charge of a negatively charged charged amino acid (glutamic acid, aspartic acid) is -1, and the other amino acids are 0. There is such a method. In addition, the charge of each amino acid residue can be determined by the existing quantum chemical calculation method based on the three-dimensional structure information of the protein registered in the protein structure database or the three-dimensional structure information obtained by the simulation method.
[0048]
There are various methods for calculating the total energy of a protein. For example, molecular dynamics and molecular dynamics described in "Introduction to Computational Chemistry" (Frank, Jensen, John Wiley & Sons, 1999) and the like are described. It can also be carried out using a method such as an energy calculation method such as a molecular orbital method or a density functional method, and an optimum one may be selected depending on the prediction accuracy required from any of the methods and the calculation environment of the operator. Alternatively, the energy of each amino acid residue can be determined by using the Fragment MO method (Chemical Physics Letters, Volume 336, Issues 1-2, 9 March 2001, Pages 163-170). This method requires a long calculation time, but is expected to have high prediction accuracy.
[0049]
As another method that does not require calculation time, there is a method of calculating electrostatic energy as follows.
E_total= {1/2} q_iq_j/ R_ij
(I and j are arbitrary amino acid residue numbers of all amino acid residues, i not j)
In this formula, E_totalIs the total energy of the protein, q_iIs the partial charge of amino acid residue i, q_jIs the partial charge of amino acid residue j, r_ijIs the spatial distance between amino acid residue i and amino acid residue j.
[0050]
The method according to this formula has a very small calculation load as compared with other methods, and is particularly effective for comprehensive calculation.
[0051]
Next, the present invention calculates the interaction energy between a specific amino acid and other amino acid residues in a protein by the following formula to determine how much each amino acid residue stabilizes the total energy of the protein. (Step SA-3).
E_interaction(N) = q_NΣq_j/ R
E_total= 1 / 2ΣE_interaction(N)
Here, N is an arbitrary amino acid residue number, E_interaction(N) is the interaction energy between amino acid residue N and other amino acid residues, j is the amino acid residue number other than N, q_NIs the partial charge of amino acid residue N, q_jRepresents the partial charge of amino acid residue j, and r represents the spatial distance between amino acid residue N and amino acid residue j. Here, half of the total interaction energy for all amino acid residues is the energy E of the whole protein._totalIs equivalent to
[0052]
Next, the present invention converts amino acid residues having a relatively high interaction energy determined in step SA-3 or amino acid residues having an interaction energy exceeding a predetermined threshold value into energetically unstable amino acids. The binding site is predicted by specifying the residue (Step SA-4).
[0053]
FIG. 2 is a diagram for explaining the concept of predicting a binding site when a complex is formed by a plurality of proteins from the amino acid sequence information of the proteins according to the present invention.
[0054]
First, the present invention assumes amino acid residues (binding residues) to be binding sites on a plurality of amino acid sequences (step SB-1). Here, FIG. 7 is a diagram showing a concept in a case where binding residues are assumed on a plurality of amino acid sequences. In the example shown in FIG. 7, it is assumed that the 50th amino acid residue of the amino acid sequence A and the 100th amino acid residue of the amino acid sequence B are binding residues. Here, as the binding residue, an amino acid residue predicted to be a binding site in each amino acid sequence by the method of the present invention described above with reference to FIG. 1 may be used.
[0055]
Next, the present invention determines a spatial distance between two amino acid residues present on different amino acid sequences (step SB-2). Here, the above three methods can be used as a method of determining the distance in the space, but the following is the method that can perform the calculation efficiently with the least calculation load. 1) The high-speed calculation method is used. The case will be described.
[0056]
First, the sequence distance between two amino acid residues existing on different amino acid sequences is defined as follows.
(Sequence distance d between the residue of interest d) = (| distance on the sequence between the residue of interest on the sequence A and the binding residue | + | distance on the sequence between the residue of interest on the sequence B and the binding residue ｜)
Here, FIG. 8 is a diagram for explaining the concept of the residue of interest. As shown in FIG. 8, a binding residue of two amino acid sequences (A and B) and an arbitrary residue of interest other than the binding residue are defined.
[0057]
Next, the present invention estimates the spatial distance r of the three-dimensional structure of the complex from the sequence distance d between two amino acid residues present on different amino acid sequences (step SB-3).
r = k dⁿ(0 <n <1)
Here, r is a distance in space, d is a distance in the array, and k is a proportional constant. Here, n is 0 to 1, preferably 0.5 to 0.6. Also, k is in the range of 2.8 to 4.8, preferably in the range of 3.3 to 4.3. That is, if the distance d on the array is known, the distance r on the space can be calculated.
[0058]
In addition, when the three-dimensional structure of the complex is known, the spatial distance between amino acid residues can be accurately obtained by using the above-described 2) calculation method using structural data.
[0059]
In addition, by using the above-mentioned 3) simulation data utilization calculation method, the three-dimensional structure of the complex is predicted, and by using the simulation data, the spatial distance between amino acid residues can be determined to some extent accurately. Can be. Here, FIG. 12 is a diagram showing a concept in a case where a composite structure is generated using docking simulation. As shown in FIG. 12, a docking simulation is performed to generate a complex structure using a plurality of three-dimensional structure information. For the docking simulation, various known simulation methods can be used. For example, as shown in FIG. 12, it is common to change the distance and orientation of two proteins. As a more specific example, one structure is fixed, and the other structure is given two degrees of freedom by rotation and two degrees of translation to generate various structures. Extracting the structure under the condition that the two structures do not overlap but come into contact provides a possible complex structure.
[0060]
Next, the present invention calculates the total energy of the protein according to the distance data in space and the charge of each amino acid (step SB-4).
[0061]
Here, various methods for determining the charge of the amino acid can be considered. For example, as described above, the charge of a positively charged charged amino acid (lysine, arginine) is 1, the charge of a negatively charged charged amino acid (glutamic acid, aspartic acid) is -1, and the other is -1. There is a method in which the charge of an amino acid is set to 0. Further, as described above, based on the three-dimensional structure information of the complex registered in the protein structure database and the three-dimensional structure information of the complex obtained by the simulation method, each amino acid residue can be determined by the existing quantum chemical calculation method. The charge can also be determined.
[0062]
Various methods can be used for calculating the total energy of a protein. As described above, for example, as described above, “Introduction to Computational Chemistry” (Frank, Jensen, John Wiley, Sons, Inc., 1999), etc. It can also be performed using methods such as energy calculation methods such as mechanics, molecular dynamics, molecular orbital method, density functional method, etc., and the most suitable one depends on the prediction accuracy required from either method and the operator's calculation environment You can choose. In addition, as described above, the energy of each amino acid residue can be obtained by using the Fragment MO method (Chemical Physics Letters, Volume 336, Issues 1-2, 9 March 2001, Pages 163-170). This method requires a long calculation time, but is expected to have high prediction accuracy.
[0063]
As another method that does not require calculation time, as described above, there is a method of calculating electrostatic energy as follows.
E_total= {1/2} q_iq_j/ R_ij
(I and j are arbitrary amino acid residue numbers of all amino acid residues, i not j)
In this formula, E_totalIs the total energy of the protein, q_iIs the partial charge of amino acid residue i, q_jIs the partial charge of amino acid residue j, r_ijIs the spatial distance between amino acid residue i and amino acid residue j. As described above, this method basically proceeds in the same procedure as the processing flow indicated by the double line, and repeats while changing the amino acid sequence of the candidate protein. Among them, the one that can form the most stable complex predicts that the probability of the interaction partner is high.
[0064]
Next, the present invention returns to step SB-1 and changes the interacting amino acid residues (binding residues) to obtain E for all combinations._totalAnd calculate the most E_totalIs predicted as the binding site (step SB-5).
[0065]
[System configuration]
First, the configuration of the present system will be described. FIG. 3 is a block diagram showing an example of the configuration of the present system to which the present invention is applied, and conceptually shows only those parts of the configuration related to the present invention. This system is configured by connecting a binding site predicting apparatus 100 and an external system 200 that provides an external database or sequence information or the like for an external program such as homology search via a network 300 so as to be communicable. Have been.
[0066]
In FIG. 3, a network 300 has a function of interconnecting the binding site prediction device 100 and the external system 200, and is, for example, the Internet.
[0067]
In FIG. 3, an external system 200 is interconnected with the binding site predicting apparatus 100 via a network 300, and provides the user with an external database on amino acid sequence information, protein three-dimensional structure information, and the like, such as homology search and motif search. It has a function of providing a website for executing an external program.
[0068]
Here, the external system 200 may be configured as a WEB server, an ASP server, or the like, and its hardware configuration may be configured by an information processing device such as a generally-available workstation, a personal computer, and its accompanying devices. Good. Each function of the external system 200 is realized by a CPU, a disk device, a memory device, an input device, an output device, a communication control device, and the like in a hardware configuration of the external system 200, a program for controlling them, and the like.
[0069]
In FIG. 3, the binding site prediction device 100 includes a control unit 102 such as a CPU that comprehensively controls the entirety of the binding site prediction device 100 and a communication device (not shown) such as a router connected to a communication line or the like. ), An input / output control interface unit 108 connected to the input device 112 and the output device 114, and a storage unit 106 for storing various databases and tables. These units are communicably connected via an arbitrary communication path. Further, the binding site prediction device 100 is communicably connected to the network 300 via a communication device such as a router and a wired or wireless communication line such as a dedicated line.
[0070]
Various databases and tables (amino acid sequence database 106a to processing result file 106g) stored in the storage unit 106 are storage means such as a fixed disk device, and various programs, tables, files, databases, and webs used for various processing. Stores page files and the like.
[0071]
Among these constituent elements of the storage unit 106, the amino acid sequence database 106a is a database that stores amino acid sequences. The amino acid sequence database 106a may be an external amino acid sequence database accessed via the Internet, and may copy these databases, store original sequence information, and store unique annotation information. The database may be an in-house database created by adding.
[0072]
The protein structure database 106b is a database that stores information on the three-dimensional structure of proteins. The protein structure database 106b may be an external three-dimensional structure information database accessed via the Internet, and may copy these databases, store original three-dimensional structure information, and further provide unique annotation information. The database may be an in-house database that is created by adding data or the like.
[0073]
The distance data file 106c is a distance information storage unit that stores information on the distance between each amino acid residue contained in the amino acid sequence (sequence distance, space distance) and the like.
[0074]
The total energy data file 106d is a total energy data storage unit that stores information on the total energy of the protein and the like.
[0075]
The interaction energy data file 106e is an interaction energy data storage unit that stores information on the interaction energy of each amino acid residue.
[0076]
The complex structure data file 106f is a complex structure data storage unit that stores information on a complex structure of a plurality of proteins.
[0077]
The processing result file 106g is a processing result storage unit that stores information on various processing results by the binding site prediction apparatus 100 and the like.
[0078]
In FIG. 3, the communication control interface unit 104 controls communication between the binding site prediction device 100 and the network 300 (or a communication device such as a router). That is, the communication control interface unit 104 has a function of communicating data with another terminal via a communication line.
[0079]
3, the input / output control interface unit 108 controls the input device 112 and the output device 114. Here, as the output device 114, in addition to a monitor (including a home television), a speaker can be used (in the following, the output device 114 may be described as a monitor). As the input device 112, a keyboard, a mouse, a microphone, and the like can be used. The monitor also realizes a pointing device function in cooperation with the mouse.
[0080]
In FIG. 3, the control unit 102 has a control program such as an OS (Operating System), a program defining various processing procedures and the like, and an internal memory for storing required data. And information processing for executing various processes. The control unit 102 functionally includes an amino acid sequence data acquisition unit 102a, a spatial distance determination unit 102b, a charge determination unit 102c, an energy calculation unit 102d, a candidate amino acid residue determination unit 102e, a complex structure generation unit 102f, an energy minimum And a binding candidate data obtaining unit 102h, a binding site predicting unit 102i, and a binding partner candidate determining unit 102j.
[0081]
Among these, the amino acid sequence data acquisition unit 102a includes an amino acid sequence data acquisition unit that acquires amino acid sequence data of a target protein or a physiologically active polypeptide, and an amino acid sequence that acquires amino acid sequence data of a plurality of target proteins or a physiologically active polypeptide. A sequence data obtaining means, and an amino acid sequence data obtaining means for obtaining amino acid sequence data of a target protein or a biologically active polypeptide and amino acid sequence data of a plurality of proteins or biologically active polypeptides as binding candidates.
[0082]
The spatial distance determining unit 102b is configured to determine a spatial distance between each amino acid residue included in the amino acid sequence data obtained by the amino acid sequence data obtaining unit, and to obtain a spatial distance by the amino acid sequence data obtaining unit. Spatial distance determining means for determining a spatial distance between each amino acid residue included in the plurality of amino acid sequence data obtained according to the three-dimensional structure information of the complex generated by the complex structure generating means, and amino acid sequence data The spatial distance between each amino acid residue contained in the target amino acid sequence data obtained by the obtaining means and the amino acid sequence data of the binding candidate is determined according to the three-dimensional structure information of the complex generated by the complex structure generating means. This is a spatial distance determining means. Here, as shown in FIG. 4, the spatial distance determination unit 102b includes a high-speed calculation unit 102k, a structural data use calculation unit 102m, and a simulation data use calculation unit 102n. Here, the high-speed calculation unit 102k is a high-speed calculation unit that determines a spatial distance by a high-speed calculation method. The structural data use calculating unit 102m is a structural data use calculating unit that determines a spatial distance by a structural data use calculation method. The simulation data use calculation unit 102n is a simulation data use calculation unit that determines a spatial distance by a simulation data use calculation method.
[0083]
In addition, the charge determination unit 102c includes a charge determination unit that determines the charge of each amino acid residue included in the amino acid sequence data, a charge determination unit that determines the charge of each amino acid residue included in the plurality of amino acid sequence data, Further, it is a charge determination means for determining the charge of each amino acid residue contained in the target amino acid sequence data and the amino acid sequence data of the binding candidate.
[0084]
In addition, the energy calculation unit 102d calculates the value of each amino acid residue according to the spatial distance between each amino acid residue determined by the spatial distance determining means and the charge of each amino acid residue determined by the charge determining means. Energy calculation means for calculating energy. As shown in FIG. 5, the energy calculator 102d includes a total energy calculator 102p and an interaction energy calculator 102q. Here, the total energy calculation unit 102p is a total energy calculation unit that calculates the total energy of the protein. The interaction energy calculator 102q is an interaction energy calculator that calculates the interaction energy of amino acid residues.
[0085]
In addition, the candidate amino acid residue determining unit 102e determines the sum of the energy by the candidate amino acid residue determining unit that determines the candidate amino acid residue to be a binding site according to the energy calculated by the energy calculating unit, and the energy minimizing unit. This is a candidate amino acid residue determining means for determining the minimum binding site as a candidate amino acid residue of the binding site.
[0086]
Further, the complex structure generating unit 102f includes a complex structure generating means for generating three-dimensional structure information of a complex in which a plurality of target proteins or physiologically active polypeptides are bound, and a target protein or biologically active polypeptide; This is a complex structure generating means for generating three-dimensional structure information of a complex to which a protein or a physiologically active polypeptide as a binding candidate is bound.
[0087]
Also, the energy minimizing unit 102g generates three-dimensional structure information of the complex by changing the binding site of the complex by the complex structure generating means, calculates the energy of each amino acid residue by the energy calculating means, and calculates the energy of the energy. This is energy minimization means for finding a binding site that minimizes the sum.
[0088]
The binding candidate data acquisition unit 102h is a binding candidate data acquiring unit that acquires amino acid sequence data and the like of a protein that is a binding candidate.
[0089]
The binding site prediction unit 102i is a binding site prediction unit that predicts the amino acid residue of the binding site from the candidate amino acid residue of the binding site.
[0090]
The binding partner candidate determining unit 102j is a binding candidate determining unit that determines a binding candidate having a binding site that minimizes the sum of energy as a result of executing the energy minimizing unit for all the binding candidates.
Details of the processing performed by these units will be described later.
[0091]
[System processing]
Next, an example of the processing of the present system configured as described above according to the present embodiment will be described in detail with reference to FIGS.
[0092]
FIG. 9 is a flowchart illustrating an example of processing of the present system in the present embodiment. In FIG. 9, the processing flow indicated by the dotted line indicates the processing flow when the binding site in one protein sequence is predicted by the present system, and the processing flow indicated by the double line may interact with the present system. The processing flow in the case of predicting the binding site using the amino acid sequences of a plurality of known proteins is shown. The processing flow indicated by the solid line shows the candidate protein that binds best to the target protein by this system. The processing flow in the case of prediction is shown. The basic concept of these three processing flows and most of the calculation processing are common. Furthermore, the general purpose of analyzing interaction information is common.
[0093]
[Process for Predicting Binding Site in One Protein Sequence]
Next, details of a process for predicting a binding site in a sequence of one protein by the present system will be described with reference to FIG. 9 and the like. The processing flow indicated by the dotted line in FIG. 9 is a flowchart illustrating an example of processing when the binding site in the sequence of one protein is predicted by the present system in the present embodiment.
[0094]
First, the binding site predicting apparatus 100 accesses the external database of the external system 200 such as Genbank or the amino acid sequence database 106a by the processing of the amino acid sequence data obtaining unit 102a, and obtains the amino acid sequence of the target protein or physiologically active polypeptide. Data is acquired (step SC-1).
[0095]
Then, the binding site prediction device 100 determines the spatial distance between each amino acid residue included in the amino acid sequence data acquired in step SC-1 by the processing of the spatial distance determining unit 102b (step SC- 2).
[0096]
Here, the spatial distance determination unit 102b may determine the spatial distance from the sequence distance between each amino acid residue by the above-described high-speed calculation method by the processing of the high-speed calculation unit 102k. The spatial distance between each amino acid residue may be determined using the known structure data by the above-described structure data use calculation method by the use of the simulation data use calculation unit 102n. The spatial distance between each amino acid residue may be determined using the prediction structure based on the processing result of the existing structure simulation program by the above-described simulation data utilization calculation method.
[0097]
Next, the binding site prediction device 100 determines the charge of each amino acid residue included in the amino acid sequence data by the processing of the charge determining unit 102c (Step SC-3). There are various methods for determining the charge of the amino acid. In general, a method in which a positively charged charged amino acid (lysine, arginine) is 1; a negatively charged charged amino acid (glutamic acid, aspartic acid) is -1; There is. The charge can also be determined by quantum chemical calculation based on the obtained three-dimensional structure information. Furthermore, if experimental data on the charge of each amino acid residue is experimentally known, it is preferable to reflect that.
[0098]
Next, the binding site prediction device 100 calculates the energy of each amino acid residue according to the determined spatial distance between each amino acid residue and the charge of each amino acid residue by the processing of the energy calculation unit 102d. (Step SC-4).
[0099]
Here, there are various methods of energy calculation, and a method of calculating electrostatic energy, which is the method that requires the least calculation time, will be described below.
First, the total energy of the protein is calculated by the following equation by the processing of the total energy calculation unit 102p.
E_total= {1/2} q_iq_j/ R_ij
(I and j are arbitrary amino acid residue numbers of all amino acid residues, i not j)
In this formula, E_totalIs the total energy of the protein, q_iIs the partial charge of amino acid residue i, q_jIs the partial charge of amino acid residue j, r_ijIs the spatial distance between amino acid residue i and amino acid residue j.
[0100]
Next, the interaction energy calculation unit 102q calculates the interaction energy between a specific amino acid and other amino acid residues in the protein according to the following formula, and calculates how much the total energy of each amino acid residue is in the protein. Find out if it has stabilized.
E_interaction(N) = q_NΣq_j/ R
E_total= 1 / 2ΣE_interaction(N)
Here, N is an arbitrary amino acid residue number, E_interaction(N) is the interaction energy between amino acid residue N and other amino acid residues, j is the amino acid residue number other than N, q_NIs the partial charge of amino acid residue N, q_jRepresents the partial charge of amino acid residue j, and r represents the spatial distance between amino acid residue N and amino acid residue j. Here, half of the total interaction energy for all amino acid residues is the energy E of the whole protein._totalIs equivalent to
[0101]
Then, the binding site prediction device 100 determines a candidate amino acid residue to be a binding site according to the calculated interaction energy by the processing of the candidate amino acid residue determination unit 102e (step SC-5). That is, the candidate amino acid residue determining unit 102e regards an amino acid residue having a relatively high interaction energy or an amino acid residue having an interaction energy exceeding a predetermined threshold as an energetically unstable amino acid residue. By specifying, a candidate amino acid residue to be a binding site is determined.
[0102]
Then, the binding site prediction device 100 predicts the binding site by removing candidates that are not spatially or energetically binding sites from the candidate amino acid residues by the processing of the binding site prediction unit 102i. For example, assuming that a result as shown in FIG. 10 is obtained as an example of the energy of the candidate amino acid residue of the processing result, the binding site prediction unit 102i selects glutamic acid (GLU) having the highest energy in FIG. Is predicted as a candidate for the binding site. In addition, the binding site prediction unit 102i, for example, as shown in FIG. 11, indicates that a portion where the three-dimensionally unstable portion is clustered (the amino acid residue portion shown in black) is likely to be a binding site. Predict.
This completes the processing for predicting the binding site in the sequence of one protein by the present system.
[0103]
[Process for Predicting Binding Site Using Amino Acid Sequences of Multiple Proteins Known to Interact]
Next, details of a process for predicting a binding site using amino acid sequences of a plurality of proteins known to interact with the present system will be described with reference to FIG. 9 and the like. The processing flow indicated by the double line in FIG. 9 is a flowchart illustrating an example of processing when predicting a binding site using the amino acid sequences of a plurality of proteins that are known to interact with the system according to the present embodiment. is there.
[0104]
First, the binding site predicting apparatus 100 accesses the external database of the external system 200 such as Genbank or the amino acid sequence database 106a by the processing of the amino acid sequence data obtaining unit 102a, and obtains the amino acid sequence of the target protein or physiologically active polypeptide. Data is acquired (step SC-1).
[0105]
Next, the binding site prediction apparatus 100 generates three-dimensional structure information of the complex in which a plurality of target proteins or physiologically active polypeptides are bound by the processing of the complex structure generating unit 102f (step SC-7). Here, as described above with reference to FIG. 12, the complex structure generating unit 102f may predict the three-dimensional structure of the complex by using a simulation data utilization calculation method. If the three-dimensional structure of the complex is known, the complex structure generating unit 102f may acquire the three-dimensional structure information of the complex.
[0106]
In addition, as described above, the complex structure generation unit 102f assumes the amino acid residues (binding residues) to be the binding sites on the plurality of amino acid sequences, without actually generating the complex structure. Processing can proceed. Here, FIG. 7 is a diagram showing a concept in a case where binding residues are assumed on a plurality of amino acid sequences. In the example shown in FIG. 7, it is assumed that the 50th amino acid residue of the amino acid sequence A and the 100th amino acid residue of the binding site prediction device for the amino acid sequence B are the binding residues. Here, the binding residue may be an amino acid residue predicted to be a binding site in each amino acid sequence by the method of the present invention described above.
[0107]
Next, the binding site prediction device 100 determines the spatial distance between each amino acid residue included in the acquired plurality of amino acid sequence data by the processing of the spatial distance determination unit 102b according to the three-dimensional structure information of the complex. (Step SC-2).
[0108]
Here, the three methods described above can be used as a method of determining the distance in space. However, when the three-dimensional structure of the complex is known or when docking simulation is performed, the spatial distance determination unit is used. 102b can accurately determine the spatial distance between amino acid residues. Hereinafter, a description will be given of a case where the calculation load is the least and the calculation can be performed efficiently.
[0109]
First, the spatial distance determination unit 102b defines a sequence distance between two amino acid residues existing on different amino acid sequences as follows.
(Sequence distance d between the residue of interest d) = (| distance on the sequence between the residue of interest on the sequence A and the binding residue | + | distance on the sequence between the residue of interest on the sequence B and the binding residue ｜)
Here, FIG. 8 is a diagram for explaining the concept of the residue of interest. As shown in FIG. 8, a binding residue of two amino acid sequences (A and B) and an arbitrary residue of interest other than the binding residue are defined.
[0110]
Next, the spatial distance determination unit 102b estimates the spatial distance r of the three-dimensional structure of the complex from the sequence distance d between two amino acid residues present on different amino acid sequences.
r = k dⁿ(0 <n <1)
Here, r is a distance in space, d is a distance in the array, and k is a proportional constant. Here, n is 0 to 1, preferably 0.5 to 0.6. Also, k is in the range of 2.8 to 4.8, preferably in the range of 3.3 to 4.3.
[0111]
Next, the binding site prediction device 100 determines the charge of each amino acid residue included in the plurality of amino acid sequence data by the processing of the charge determination unit 102c (step SC-3).
[0112]
Next, the binding site prediction apparatus 100 calculates the distance between the amino acid residues determined in step SC-2 and the respective amino acid residues determined in step SC-3 by the processing of the energy calculation unit 102d. The energy of each amino acid residue is calculated according to the charge (step SC-4).
[0113]
Then, the binding site prediction device 100 determines a candidate amino acid residue to be a binding site according to the calculated interaction energy by the processing of the candidate amino acid residue determination unit 102e (step SC-5).
[0114]
Then, the binding site predicting apparatus 100 changes the binding site of the complex in step SC-7 to generate the three-dimensional structure information of the complex by the processing of the energy minimizing unit 102g, and generates each amino acid residue in step SC-4. Is calculated, and the binding site where the sum of the energies is minimized is determined (the steps from Step SC-7 to Step SC-5 are repeated as appropriate).
[0115]
Then, the binding site predicting apparatus 100 determines, by the processing of the candidate amino acid residue determining unit 102e, the binding site that finally has the minimum total energy as the candidate amino acid residue of the binding site (step SC-5). . Here, the candidate amino acid residue determining unit 102e may create a diagram in which the total sum of the energies of the proteins is plotted based on the amino acid sequence, and output the diagram to the output device 114. FIG. 13 is an example of a diagram plotting the total energy when each amino acid residue of protein A and protein B is a binding residue. By creating the plot in this way, it becomes possible to visually grasp which amino acid residue of the two amino acid sequences is selected as the binding residue and the total energy is reduced.
This completes the process of predicting a binding site using the amino acid sequences of a plurality of proteins known to interact with the present system.
[0116]
[Process for Predicting Candidate Protein on the Other Side that Best Binds to Target Protein]
Next, details of a process for predicting a candidate protein on the partner side that best binds to a target protein by the present system will be described with reference to FIG. 9 and the like. The processing flow indicated by the solid line in FIG. 9 is a flowchart illustrating an example of processing in a case where the present system in the present embodiment predicts a candidate protein on the partner side that best binds to a target protein.
[0117]
First, the binding site predicting apparatus 100 accesses the external database of the external system 200 such as Genbank or the amino acid sequence database 106a by the processing of the amino acid sequence data obtaining unit 102a, and obtains the amino acid sequence of the target protein or biologically active polypeptide. Data is acquired (step SC-1). In addition, the binding site prediction apparatus 100 accesses the external database of the external system 200 such as Genbank or the amino acid sequence database 106a by the processing of the binding candidate data acquisition unit 102h, and obtains one or more candidate binding candidates for the target protein. The amino acid sequence data of a plurality of proteins or physiologically active polypeptides is obtained (Step SC-6).
[0118]
Next, the binding site prediction apparatus 100, by the processing of the complex structure generating unit 102f, obtains the three-dimensional structure information of the complex in which the target protein or bioactive polypeptide and the candidate protein or bioactive polypeptide are bound. Generate (Step SC-7).
[0119]
Next, the binding site prediction apparatus 100 includes the target amino acid sequence data obtained in step SC-1 and the amino acid sequence data of the binding candidate obtained in step SC-6 by the processing of the spatial distance determination unit 102b. The spatial distance between each amino acid residue to be determined is determined according to the three-dimensional structure information of the complex generated in step SC-7 (step SC-2).
[0120]
Next, the binding site prediction apparatus 100 determines the charge of each amino acid residue included in the target amino acid sequence data and the amino acid sequence data of the binding candidate by the processing of the charge determining unit 102c (step SC-3).
[0121]
Next, the binding site predicting apparatus 100 calculates, by the processing of the energy calculating unit 102d, the spatial distance between each amino acid residue determined in step SC-2 and each amino acid residue determined in step SC-3. The energy of each amino acid residue is calculated according to the charge (step SC-4).
[0122]
Next, the binding site prediction apparatus 100 generates the three-dimensional structure information of the complex by changing the binding site in the complex in step SC-7 by the processing of the energy minimizing unit 102g, and generates each amino acid residue in step SC-4. Is calculated, and a binding site where the sum of the energies is minimized is obtained (steps SC-7 to SC-5 are repeated as appropriate).
[0123]
Next, the binding site prediction apparatus 100 repeats steps SC-6 to SC-5 for all binding candidates by the processing of the candidate amino acid residue determining unit 102e, and executes the energy minimization processing. Is determined (Step SC-8).
This completes the processing for predicting the candidate protein on the partner side that best binds to the target protein by the present system.
[0124]
[Example of the present invention]
Next, details of the embodiment of the present invention will be described with reference to FIGS.
[0125]
[Example 1 of the present invention; ribonuclease A]
Next, details of the first embodiment of the present invention will be described with reference to FIGS. Example 1 relates to prediction of a binding site of a single protein.
Ribonuclease A, a hydrolase, is a protein that has been well studied experimentally. Since the structure of the complex of ribonuclease A and its inhibitor is known, the binding site is specified on the amino acid sequence.
First, the amino acid sequence data of ribonuclease A was obtained from the protein sequence database Genbank.
[0126]
Then, distance information of amino acids was estimated from the amino acid sequence data of ribonuclease A by the following method. First, the relationship between the distance in sequence and the distance in space was determined for each type of amino acid from the three-dimensional structure information of all the proteins or polypeptides registered in PDB (Protein Data Bank). For example, FIG. 14 is a diagram showing the relationship between the distance in the arrangement of two glutamic acids and the distance in space. As shown in FIG. 14, for example, it is known by a known statistical method that the average of the spatial distance when glutamic acid and glutamic acid are separated by 20 residues on the sequence is 20 °. As described above, information indicating the relationship between the distance in sequence between amino acid residues and the distance in space was obtained.
[0127]
Then, the charge of the amino acid was determined. Here, a charge is assigned to each amino acid residue, such as −1 for glutamic acid and aspartic acid, +1 for arginine, lysine and histidine, and 0 for others.
[0128]
Then, the interaction energy of each amino acid residue was calculated as follows.
E_interaction(K) = q_KΣq_j/ R
(Where K is the amino acid residue number, E_interaction(K) is the interaction energy between amino acid residue K and the other, j is any amino acid residue other than K, and r is the spatial distance between amino acid residue K and amino acid residue j.
[0129]
Then, the energy of each amino acid residue of ribonuclease A was calculated by the above equation, and the energy of each amino acid residue of ribonuclease A was plotted against the amino acid residue number. FIG. 15 is a diagram in which the energy of each amino acid residue of ribonuclease A is plotted against the amino acid residue number.
[0130]
Then, those in which the amino acid residues of ribonuclease A had an energy of 0 or more were summarized in the table as binding site candidates (FIG. 16). As shown in FIG. 16, of the 18 candidate binding sites, the actual number of binding sites (experimentally determined binding sites) was 12. As described above, according to the present invention, it was possible to predict a binding site with very high accuracy and high speed using only the amino acid sequence information of ribonuclease A.
This ends the first embodiment of the present invention.
[0131]
[Example 2 of the present invention; acetylcholine esterase inhibitor]
Next, the details of the second embodiment of the present invention will be described with reference to FIGS. Example 2 also relates to the prediction of the binding site of a single protein.
In Example 2, the binding site was estimated based on the amino acid sequence of acetylcholine esterase inhibitor. Here, the existing three-dimensional structure information data included in the PDB was used instead of performing the three-dimensional structure prediction.
[0132]
FIG. 17 is a diagram showing a part of the three-dimensional structure information data of the acetylcholine esterase inhibitor stored in the PDB. The atomic numbers, atomic species, chain names, amino acid residue numbers, X coordinates, Y coordinates, and Z coordinates are shown from the second column of FIG.
[0133]
For example, the spatial distance R between amino acid residue number I and amino acid residue number J_IJRepresents coordinates (x) of the amino acid residue number I such as the center of gravity or a specific main chain atom._I, Y_I, Z_I), And coordinates such as the center of gravity of amino acid residue number J and atoms of a specific main chain are (x_J, Y_J, Z_J) Can be calculated as follows.
R_IJ ²= (X_I-X_J)²+ (Y_I-Y_J)²+ (Z_I-Z_J)²
(Where R_IJ> 0)
[0134]
More specifically, when the spatial distance between glutamic acid at amino acid residue number 4 and aspartic acid at amino acid residue number 5 shown in FIG. 17 is calculated from the distance between the atoms of α-carbon, the following is obtained. .

[0135]
FIG. 18 is a diagram showing the energy of acetylcholinesterase inhibitor obtained according to the present invention. From FIG. 18, ten acetylcholine esterase inhibitor energies having an energy of 0 or more were taken out as candidate binding sites, and whether or not they were actually binding sites was experimentally examined. Among them, seven were actually binding sites. (FIG. 19).
[0136]
As described above, the binding site can be predicted with extremely high accuracy. The second embodiment is different from the first embodiment in that known three-dimensional structure information is used. In other words, although the method of determining the spatial distance is changed between the first embodiment and the second embodiment, the effect of the present invention can be obtained by using any method of determining the spatial distance since both have given good results. It can be expected.
Thus, the second embodiment of the present invention is completed.
[0137]
[Example 3 of the present invention; complex of "huntingtin-associated \ protein \ interacting \ protein" and "nitric \ oxide \ synthase \ 2A"]
Next, a third embodiment of the present invention will be described in detail with reference to FIG. Example 3 relates to prediction of a binding site when two proteins bind. It has been experimentally found that "huntingtin-associated @ protein @ interacting @ protein" binds to "nitric @ oxide @ synthase @ 2A". Further, it is known that the binding site "huntingtin-associated @ protein @ interacting @ protein" is around amino acid residue number 600, and "nitric @ oxidase synthesis @ 2A" is around amino acid residue number 100.
[0138]
Here, in the present embodiment, acquisition of sequence information, prediction of a three-dimensional structure, and determination of charges were performed in the same manner as in the first embodiment. However, the method of converting the amino acid sequence distance into the spatial distance is based on the assumption that the protein takes a Gaussian chain, and the sequence distance and the spatial distance are related by the following formula.
r = 3.8 d^0.5
Here, r is the distance in space, and d is the distance in the array.
[0139]
The complex structure was generated using the high-speed calculation method described above. That is, the following equation was used.
(Distance in space) = {k (| Distance in sequence between target residue and binding residue on A | + | Distance in sequence between target residue and binding residue on B |)}ⁿ
[0140]
Then, the energy of the complex assuming each binding site was calculated, and FIG. 20 could be created. Here, in FIG. 20, the horizontal axis represents the amino acid residue number of the binding site of huntingtin-associated {protein} interacting protein, the vertical axis represents the amino acid residue number of the binding site of nitric oxide synthase 2A, and the complex at each binding site. It is a contour line showing the sum of energy when a body is generated.
[0141]
According to FIG. 20, for example, the energy of the complex in the case where the amino acid residue No. 500 of huntingtin-associated @ protein @ interacting @ protein and the amino acid residue 150 of nitric oxide @ synthase @ 2A are a binding site is -10, The energy for each binding site is determined.
[0142]
As shown in FIG. 20, there are two minimum parts of energy. One is that the binding site of huntingtin-associated {protein} interacting protein is near amino acid residues 600 to 950, and the binding site of nitricoxide side synthase 2A is amino acid residue 25 to In the case of binding at around 100, the other one was at a binding site of huntingtin-associated {protein} interacting protein at around amino acid residues 650 to 900, and at a binding site of nitric oxide, synthase 2A at around amino acid residues 475 to 500. Is the case.
[0143]
Here, the former corresponds to the actual binding site (the portion surrounded by a black circle in the figure). As described above, the binding sites of the two proteins could be accurately predicted.
Thus, the third embodiment of the present invention is completed.
[0144]
[Embodiment 4 of the present invention; E2F transcript factor1] Next, details of Embodiment 4 of the present invention will be described with reference to FIG.
Embodiment 4 relates to the binding partner prediction. E2F transcription description factor 1 (hereinafter, E2F1) is a protein whose information on the interaction partner is well examined experimentally.
[0145]
Here, a partner interacting with E2F1 was searched from the database of Homo @ Sapiens genes (here, 6,600 were randomly extracted) and used as amino acid sequence data of the candidate protein.
[0146]
Then, similarly to the procedure calculated in Example 3, a binding site to E2F1 is searched for each candidate protein of the partner. Then, the energy when the energy is most stable (minimum) is defined as the interaction energy. FIG. 21 is a histogram of the interaction energy of each candidate protein and the number of genes.
[0147]
As shown in FIG. 21, the relative interaction energy could be calculated. For example, there are 100 interaction energies greater than 90 (energy less than -90), but there is a high possibility that the ones here are interaction partners. This method is very fast and can comprehensively calculate the interaction.
This concludes the fourth embodiment of the present invention.
[0148]
[Other embodiments]
Although the embodiments of the present invention have been described above, the present invention is not limited to the above-described embodiments, but may be applied to various different embodiments within the scope of the technical idea described in the claims. It may be implemented.
[0149]
For example, the case where the binding site prediction apparatus 100 performs the processing in a stand-alone mode has been described as an example, but the processing is performed in response to a request from a client terminal configured in a separate housing from the binding site prediction apparatus 100, The processing result may be returned to the client terminal.
[0150]
Further, among the processes described in the embodiment, all or a part of the processes described as being performed automatically may be manually performed, or all of the processes described as being performed manually may be performed. Alternatively, it can be performed partly automatically by a known method.
In addition, the processing procedures, control procedures, specific names, information including parameters such as various registration data and search conditions, screen examples, and database configurations shown in the above-described documents and drawings, except where otherwise noted, It can be changed arbitrarily.
[0151]
Further, regarding the binding site prediction apparatus 100, each component illustrated is a functional concept and does not necessarily need to be physically configured as illustrated.
For example, with respect to the processing functions included in each unit or each device of the binding site prediction apparatus 100, particularly, each processing function performed by the control unit 102, all or any part of the processing functions are transferred to a CPU (Central Processing Unit) and the CPU. It can be realized by a program that is interpreted and executed, or can be realized as hardware by wired logic. The program is recorded on a recording medium described later, and is mechanically read by the binding site prediction device 100 as necessary.
[0152]
That is, a computer program for giving instructions to the CPU in cooperation with an OS (Operating System) and performing various processes is recorded in the storage unit 106 such as a ROM or an HD. This computer program is executed by being loaded into a RAM or the like, and configures the control unit 102 in cooperation with the CPU. Further, this computer program may be recorded in an application program server connected to the binding site prediction apparatus 100 via an arbitrary network 300, and all or a part of the computer program may be downloaded as necessary. It is.
[0153]
Further, the program according to the present invention can be stored in a computer-readable recording medium. Here, the “recording medium” refers to an arbitrary “portable physical medium” such as a flexible disk, a magneto-optical disk, a ROM, an EPROM, an EEPROM, a CD-ROM, an MO, a DVD, and the like, and a built-in various computer systems. A short-term program such as a communication line or a carrier wave when transmitting the program via an arbitrary "fixed physical medium" such as ROM, RAM, HD, or a network represented by LAN, WAN, or the Internet. "Communications medium" that holds.
[0154]
The “program” is a data processing method described in an arbitrary language or description method, and may be in any format such as a source code or a binary code. The "program" is not necessarily limited to a single program, but may be distributed as a plurality of modules or libraries, or may be operated in cooperation with a separate program represented by an OS (Operating System). Includes those that achieve functions. Note that a known configuration and procedure can be used for a specific configuration, a reading procedure, an installation procedure after reading, and the like in each apparatus described in the embodiments.
[0155]
Various databases and the like (amino acid sequence database 106a to processing result file 106g) stored in the storage unit 106 are storage devices such as a memory device such as a RAM and a ROM, a fixed disk device such as a hard disk, a flexible disk, and an optical disk. Stores various programs, tables, files, databases, web page files, and the like used for various processes and for providing a website.
[0156]
In addition, the binding site prediction apparatus 100 connects a peripheral device such as a printer, a monitor, or an image scanner to an information processing device such as a known personal computer or an information processing terminal such as a workstation, and connects the information processing device of the present invention to the information processing device. May be implemented by implementing software (including programs, data, and the like) for implementing the above.
[0157]
Furthermore, the specific form of the distribution / integration of the binding site prediction device 100 is not limited to the illustrated one, and all or a part thereof may be functionally or physically distributed / integrated in an arbitrary unit corresponding to various loads or the like. Can be integrated and configured. For example, each database may be independently configured as an independent database device, or a part of the processing may be realized by using CGI (Common Gateway Interface).
[0158]
The network 300 has a function of interconnecting the binding site prediction device 100 and the external system 200, and includes, for example, the Internet, an intranet, a LAN (including both wired / wireless), a VAN, and a personal computer. A communication network, a public telephone network (including both analog and digital), a private line network (including both analog and digital), a CATV network, an IMT2000 system, a GSM system, a PDC / PDC-P system, and the like. It may include any of a cellular line switching network / portable packet switching network, a radio paging network, a local radio network such as Bluetooth, a PHS network, and a satellite communication network such as CS, BS or ISDB. That is, the present system can transmit and receive various data via any network regardless of wired or wireless.
[0159]
【The invention's effect】
As described in detail above, according to the present invention, the spatial distance data between each amino acid residue in the three-dimensional structure of the protein or bioactive polypeptide is determined from the amino acid sequence data of the protein or bioactive polypeptide, Since the binding site is predicted by specifying an electrostatically unstable amino acid residue according to the distance data and the charge of each amino acid, it is likely to be electrostatically unstable from the amino acid sequence of the protein or the bioactive polypeptide. It is possible to provide a binding site prediction method, a binding site prediction device, a program, and a recording medium capable of quickly and accurately predicting a binding site by utilizing the fact that various amino acid residues tend to become binding sites. it can.
[0160]
According to the present invention, the amino acid sequence data of the target protein or the biologically active polypeptide is obtained, the spatial distance between each amino acid residue contained in the obtained amino acid sequence data is determined, and the amino acid sequence is determined. Determine the charge of each amino acid residue included in the data, and determine the energy of each amino acid residue according to the determined spatial distance between each amino acid residue and the determined charge of each amino acid residue. Calculate and determine candidate amino acid residues to be binding sites according to the calculated energy, so amino acid residues that are likely to be electrostatically unstable from the amino acid sequence of protein or bioactive polypeptide become binding sites. A binding site prediction method, a binding site prediction device, a program, and a record that can quickly and accurately predict a binding site using the ease of use It is possible to provide the body.
[0161]
Further, according to the present invention, obtaining amino acid sequence data of a plurality of target proteins or bioactive polypeptides, generating three-dimensional structure information of a complex in which the plurality of target proteins or bioactive polypeptides are bound, and obtaining The spatial distance between each amino acid residue contained in the plurality of amino acid sequence data determined is determined according to the three-dimensional structure information of the generated complex, and the charge of each amino acid residue contained in the plurality of amino acid sequence data is determined. According to the determined spatial distance between each amino acid residue and the determined charge of each amino acid residue, calculate the energy of each amino acid residue and change the binding site for the complex. Generates the three-dimensional structure information of the complex, calculates the energy of each amino acid residue, finds the binding site that minimizes the sum of the energies, Is determined as a candidate amino acid residue for the binding site, and the amino acid sequence which is likely to be electrostatically unstable from the amino acid sequence of the protein or the biologically active polypeptide is likely to become the binding site. Thus, it is possible to provide a binding site prediction method, a binding site prediction device, a program, and a recording medium capable of quickly and accurately predicting a binding site.
[0162]
Further, according to the present invention, the amino acid sequence data of the target protein or biologically active polypeptide and the amino acid sequence data of one or more proteins or biologically active polypeptides as binding candidates are obtained, and the target protein or biologically active polypeptide is obtained. Generates three-dimensional structure information of a complex in which a physiologically active polypeptide and a protein or a physiologically active polypeptide as a binding candidate are bound, and obtains each amino acid contained in the obtained target amino acid sequence data and the amino acid sequence data of the binding candidate. The spatial distance between the residues is determined according to the three-dimensional structure information of the generated complex, and the charge of each amino acid residue included in the target amino acid sequence data and the amino acid sequence data of the binding candidate is determined. Each amino acid residue according to the spatial distance between the determined amino acid residues and the determined charge of each amino acid residue. Calculate the energy, change the binding site for the complex, generate steric structure information of the complex, calculate the energy of each amino acid residue, find the binding site that minimizes the sum of the energies, and determine all binding candidates As a result of performing the energy minimizing process on the amino acid sequence, a binding candidate having a binding site that minimizes the total energy is determined. Therefore, amino acid residues that are likely to be electrostatically unstable from the amino acid sequence of the protein or the biologically active polypeptide are determined. Provided are a binding site prediction method, a binding site prediction device, a program, and a recording medium capable of quickly and accurately predicting an optimal binding candidate protein by utilizing the fact that a group easily becomes a binding site. Can be.
[Brief description of the drawings]
FIG. 1 is a diagram illustrating the concept of predicting a binding site of a protein from amino acid sequence information of the protein according to the present invention.
FIG. 2 is a diagram illustrating the concept of predicting a binding site when a complex is formed by a plurality of proteins from the amino acid sequence information of the proteins according to the present invention.
FIG. 3 is a block diagram illustrating an example of a configuration of the present system to which the present invention is applied.
FIG. 4 is a block diagram illustrating an example of a configuration of a spatial distance determination unit 102b to which the present invention is applied.
FIG. 5 is a block diagram illustrating an example of a configuration of an energy calculation unit 102d to which the present invention is applied.
FIG. 6 is a diagram showing the concept of the high-speed calculation method of the present invention.
FIG. 7 is a diagram showing a concept when a binding residue is assumed on a plurality of amino acid sequences.
FIG. 8 is a diagram illustrating the concept of a residue of interest.
FIG. 9 is a flowchart illustrating an example of processing of the present system in the present embodiment.
FIG. 10 is a diagram showing an example of the energy and the like of a candidate amino acid residue as a processing result.
FIG. 11 is a diagram illustrating an example of a case where unstable portions on a three-dimensional structure are clustered.
FIG. 12 is a diagram showing a concept when a composite structure is generated using docking simulation.
FIG. 13 is an example of a diagram plotting the total energy when each amino acid residue of protein A and protein B is a binding residue.
FIG. 14 is a diagram showing the relationship between the distance on the arrangement of two glutamic acids and the distance on the space.
FIG. 15 is a diagram in which the energy of each amino acid residue of ribonuclease A is plotted against the amino acid residue number.
FIG. 16 is a diagram in which ribonuclease A amino acids having an energy of 0 or more are summarized in a table as binding site candidates.
FIG. 17 is a diagram showing a part of steric structure information data of acetylcholine esterase inhibitor stored in PDB.
FIG. 18 is a graph showing the energy of acetylcholinesterase inhibitor obtained according to the present invention.
FIG. 19 is a view showing the results of taking out ten acetylcholine esterase inhibitor having an energy of 0 or more as binding site candidates and experimentally examining whether or not the binding site is an actual binding site.
FIG. 20 shows the amino acid residue number of the binding site of huntingtin-associated protein interacting protein on the horizontal axis, the amino acid residue number of the binding site of nitric oxide synthase 2A on the vertical axis, and forms the complex at each binding site. It is the figure which displayed the sum total of the energy at the time of production | generation with a contour line.
FIG. 21 is a histogram of the interaction energy of each candidate protein and the number of genes.
[Explanation of symbols]
100 binding site prediction device
102 control unit
102a @ amino acid sequence data acquisition unit
102b space distance determination unit
102c Charge determining unit
102d energy calculation unit
102e @ candidate amino acid residue determining unit
102f complex structure generator
102g energy minimizing part
102h combination candidate data acquisition unit
102i binding site prediction unit
102j Binding partner candidate determination unit
102k high-speed calculation unit
102m structure data use calculation unit
102n @ Simulation data utilization calculation unit
102p total energy calculation unit
102q interaction energy calculator
104 Communication control interface unit
106 storage unit
106a amino acid sequence database
106b @ protein structure database
106c distance data file
106d Total energy data file
106e interaction energy data file
106f complex structure data file
106g processing result file
108 I / O control interface
112 input device
114 output device
200 external system
300 network

Claims (11)

The spatial distance data between each amino acid residue in the three-dimensional structure of the protein or the biologically active polypeptide is obtained from the amino acid sequence data of the protein or the biologically active polypeptide. A binding site prediction method, wherein a binding site is predicted by specifying a stable amino acid residue. An amino acid sequence data obtaining step of obtaining amino acid sequence data of a target protein or a biologically active polypeptide,
A spatial distance determining step of determining a spatial distance between each amino acid residue included in the amino acid sequence data obtained by the amino acid sequence data obtaining step,
A charge determination step of determining the charge of each amino acid residue contained in the amino acid sequence data,
Energy calculation for calculating the energy of each amino acid residue according to the spatial distance between each amino acid residue determined in the spatial distance determination step and the charge of each amino acid residue determined in the charge determination step Steps and
According to the energy calculated by the energy calculation step, according to the candidate amino acid residue determining step of determining a candidate amino acid residue serving as a binding site,
A binding site prediction method comprising: Amino acid sequence data obtaining step of obtaining amino acid sequence data of a plurality of proteins or biologically active polypeptides of interest,
A complex structure generating step of generating three-dimensional structure information of a complex in which a plurality of proteins or physiologically active polypeptides of interest are bound,
The spatial distance between each amino acid residue included in the plurality of amino acid sequence data obtained in the amino acid sequence data obtaining step is determined according to the three-dimensional structure information of the complex generated in the complex structure generating step. A spatial distance determining step;
A charge determination step of determining the charge of each amino acid residue contained in the plurality of amino acid sequence data,
Energy calculation for calculating the energy of each amino acid residue according to the spatial distance between each amino acid residue determined in the spatial distance determination step and the charge of each amino acid residue determined in the charge determination step Steps and
By changing the binding site for the complex in the complex structure generating step, the three-dimensional structure information of the complex is generated, the energy of each amino acid residue is calculated in the energy calculation step, and the bond in which the sum of the energy is minimized is calculated. An energy minimization step for finding the site;
A candidate amino acid residue determining step of determining a binding site in which the sum of energies is minimized by the energy minimizing step as a candidate amino acid residue of the binding site,
A binding site prediction method comprising: An amino acid sequence data obtaining step of obtaining an amino acid sequence data of a target protein or a biologically active polypeptide, and one or more amino acid sequence data of a protein or a biologically active polypeptide as a binding candidate;
A complex structure generating step of generating three-dimensional structure information of a complex in which the target protein or bioactive polypeptide and the protein or bioactive polypeptide as the binding candidate are bound,
The complex generated by the complex structure generating step is a spatial distance between the target amino acid sequence data obtained in the amino acid sequence data obtaining step and each amino acid residue included in the amino acid sequence data of the binding candidate. A spatial distance determining step of determining according to the three-dimensional structure information of
A charge determination step of determining the charge of each amino acid residue contained in the amino acid sequence data of the target amino acid sequence data and the binding candidate,
Energy calculation for calculating the energy of each amino acid residue according to the spatial distance between each amino acid residue determined in the spatial distance determination step and the charge of each amino acid residue determined in the charge determination step Steps and
By changing the binding site for the complex in the complex structure generating step, the three-dimensional structure information of the complex is generated, the energy of each amino acid residue is calculated in the energy calculation step, and the bond in which the sum of the energy is minimized is calculated. An energy minimization step for finding the site;
As a result of executing the energy minimizing step for all binding candidates, a binding candidate determining step of determining a binding candidate having a binding site in which the sum of the energies is minimized,
A binding site prediction method comprising: Amino acid sequence data obtaining means for obtaining the amino acid sequence data of the protein or biologically active polypeptide of interest,
A spatial distance determining means for determining a spatial distance between each amino acid residue contained in the amino acid sequence data obtained by the amino acid sequence data obtaining means,
Charge determination means for determining the charge of each amino acid residue contained in the amino acid sequence data,
Energy calculation for calculating the energy of each amino acid residue according to the spatial distance between each amino acid residue determined by the spatial distance determining means and the charge of each amino acid residue determined by the charge determining means Means,
According to the energy calculated by the energy calculation means, candidate amino acid residue determining means for determining a candidate amino acid residue serving as a binding site,
A binding site prediction device comprising: Amino acid sequence data obtaining means for obtaining amino acid sequence data of a plurality of proteins or biologically active polypeptides of interest,
A complex structure generating means for generating three-dimensional structure information of a complex in which a plurality of proteins or physiologically active polypeptides of interest are bound,
The spatial distance between each amino acid residue included in the plurality of amino acid sequence data obtained by the amino acid sequence data obtaining means is determined according to the three-dimensional structure information of the complex generated by the complex structure generating means. Spatial distance determining means;
Charge determination means for determining the charge of each amino acid residue contained in the plurality of amino acid sequence data,
Energy calculation for calculating the energy of each amino acid residue according to the spatial distance between each amino acid residue determined by the spatial distance determining means and the charge of each amino acid residue determined by the charge determining means Means,
By changing the binding site of the complex by the complex structure generating means, the three-dimensional structure information of the complex is generated, and the energy of each amino acid residue is calculated by the energy calculating means, and the bond having the minimum total energy is calculated. An energy minimizing means for finding a part,
A candidate amino acid residue determining means for determining a binding site at which the total energy is minimized by the energy minimizing means as a candidate amino acid residue of the binding site,
A binding site prediction device comprising: An amino acid sequence data obtaining means for obtaining the amino acid sequence data of the target protein or the biologically active polypeptide and the amino acid sequence data of one or more proteins or the biologically active polypeptides as binding candidates;
A complex structure generating means for generating three-dimensional structure information of a complex in which the target protein or the biologically active polypeptide is bound to the protein or the biologically active polypeptide as the binding candidate,
The complex produced by the complex structure producing means is a spatial distance between the target amino acid sequence data acquired by the amino acid sequence data acquiring means and each amino acid residue contained in the amino acid sequence data of the binding candidate. Spatial distance determining means for determining according to the three-dimensional structure information of
Charge determination means for determining the charge of each amino acid residue contained in the amino acid sequence data of the target amino acid sequence data and the binding candidate,
Energy calculation for calculating the energy of each amino acid residue according to the spatial distance between each amino acid residue determined by the spatial distance determining means and the charge of each amino acid residue determined by the charge determining means Means,
By changing the binding site of the complex by the complex structure generating means, the three-dimensional structure information of the complex is generated, and the energy of each amino acid residue is calculated by the energy calculating means, and the bond having the minimum total energy is calculated. An energy minimizing means for finding a part,
As a result of executing the energy minimizing means for all the binding candidates, a binding candidate determining means for determining a binding candidate having a binding site that minimizes the sum of the energies,
A binding site prediction device comprising: An amino acid sequence data obtaining step of obtaining amino acid sequence data of a target protein or a biologically active polypeptide,
A spatial distance determining step of determining a spatial distance between each amino acid residue included in the amino acid sequence data obtained by the amino acid sequence data obtaining step,
A charge determination step of determining the charge of each amino acid residue contained in the amino acid sequence data,
Energy calculation for calculating the energy of each amino acid residue according to the spatial distance between each amino acid residue determined in the spatial distance determination step and the charge of each amino acid residue determined in the charge determination step Steps and
According to the energy calculated by the energy calculation step, according to the candidate amino acid residue determining step of determining a candidate amino acid residue serving as a binding site,
A program causing a computer to execute a binding site prediction method including: Amino acid sequence data obtaining step of obtaining amino acid sequence data of a plurality of proteins or biologically active polypeptides of interest,
A complex structure generating step of generating three-dimensional structure information of a complex in which a plurality of proteins or physiologically active polypeptides of interest are bound,
The spatial distance between each amino acid residue included in the plurality of amino acid sequence data obtained in the amino acid sequence data obtaining step is determined according to the three-dimensional structure information of the complex generated in the complex structure generating step. A spatial distance determining step;
A charge determination step of determining the charge of each amino acid residue contained in the plurality of amino acid sequence data,
Energy calculation for calculating the energy of each amino acid residue according to the spatial distance between each amino acid residue determined in the spatial distance determination step and the charge of each amino acid residue determined in the charge determination step Steps and
By changing the binding site for the complex in the complex structure generating step, the three-dimensional structure information of the complex is generated, the energy of each amino acid residue is calculated in the energy calculation step, and the bond in which the sum of the energy is minimized is calculated. An energy minimization step for finding the site;
A candidate amino acid residue determining step of determining a binding site in which the sum of energies is minimized by the energy minimizing step as a candidate amino acid residue of the binding site,
A program causing a computer to execute a binding site prediction method including: An amino acid sequence data obtaining step of obtaining an amino acid sequence data of a target protein or a biologically active polypeptide, and one or more amino acid sequence data of a protein or a biologically active polypeptide as a binding candidate;
A complex structure generating step of generating three-dimensional structure information of a complex in which the target protein or bioactive polypeptide and the protein or bioactive polypeptide as the binding candidate are bound,
The complex generated by the complex structure generating step is a spatial distance between the target amino acid sequence data obtained in the amino acid sequence data obtaining step and each amino acid residue included in the amino acid sequence data of the binding candidate. A spatial distance determining step of determining according to the three-dimensional structure information of
A charge determination step of determining the charge of each amino acid residue contained in the amino acid sequence data of the target amino acid sequence data and the binding candidate,
Energy calculation for calculating the energy of each amino acid residue according to the spatial distance between each amino acid residue determined in the spatial distance determination step and the charge of each amino acid residue determined in the charge determination step Steps and
By changing the binding site for the complex in the complex structure generating step, the three-dimensional structure information of the complex is generated, the energy of each amino acid residue is calculated in the energy calculation step, and the bond in which the sum of the energy is minimized is calculated. An energy minimization step for finding the site;
As a result of executing the energy minimizing step for all binding candidates, a binding candidate determining step of determining a binding candidate having a binding site in which the sum of the energies is minimized,
A program causing a computer to execute a binding site prediction method including: A computer-readable recording medium on which the program according to any one of claims 8 to 10 is recorded.

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