JP3669704B2 - 三次元構造データベースから新規リガンド化合物を検索する方法 - Google Patents

三次元構造データベースから新規リガンド化合物を検索する方法 Download PDF

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JP3669704B2
JP3669704B2 JP51445296A JP51445296A JP3669704B2 JP 3669704 B2 JP3669704 B2 JP 3669704B2 JP 51445296 A JP51445296 A JP 51445296A JP 51445296 A JP51445296 A JP 51445296A JP 3669704 B2 JP3669704 B2 JP 3669704B2
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hydrogen
trial
compound
trial compound
biopolymer
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JPWO1996013785A1 (ja
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昭子 板井
実穂 水谷
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    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16C—COMPUTATIONAL CHEMISTRY; CHEMOINFORMATICS; COMPUTATIONAL MATERIALS SCIENCE
    • G16C20/00—Chemoinformatics, i.e. ICT specially adapted for the handling of physicochemical or structural data of chemical particles, elements, compounds or mixtures
    • G16C20/40—Searching chemical structures or physicochemical data
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B15/00—ICT specially adapted for analysing two-dimensional [2D] or three-dimensional [3D] molecular structures, e.g. structural or functional relations or structure alignment
    • G16B15/30—Drug targeting using structural data; Docking or binding prediction
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B15/00—ICT specially adapted for analysing two-dimensional [2D] or three-dimensional [3D] molecular structures, e.g. structural or functional relations or structure alignment
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y10—TECHNICAL SUBJECTS COVERED BY FORMER USPC
    • Y10S—TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y10S707/00—Data processing: database and file management or data structures
    • Y10S707/99931—Database or file accessing
    • Y10S707/99933—Query processing, i.e. searching
    • Y10S707/99936—Pattern matching access
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y10—TECHNICAL SUBJECTS COVERED BY FORMER USPC
    • Y10S—TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y10S707/00—Data processing: database and file management or data structures
    • Y10S707/99941—Database schema or data structure
    • Y10S707/99944—Object-oriented database structure
    • Y10S707/99945—Object-oriented database structure processing

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  • Chemical & Material Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Theoretical Computer Science (AREA)
  • Health & Medical Sciences (AREA)
  • Physics & Mathematics (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Pharmacology & Pharmacy (AREA)
  • Biophysics (AREA)
  • Biotechnology (AREA)
  • Evolutionary Biology (AREA)
  • General Health & Medical Sciences (AREA)
  • Medical Informatics (AREA)
  • Medicinal Chemistry (AREA)
  • Computing Systems (AREA)
  • Information Retrieval, Db Structures And Fs Structures Therefor (AREA)
  • Organic Low-Molecular-Weight Compounds And Preparation Thereof (AREA)
  • Investigating Or Analysing Biological Materials (AREA)
JP51445296A 1994-10-31 1995-10-30 三次元構造データベースから新規リガンド化合物を検索する方法 Expired - Fee Related JP3669704B2 (ja)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
JP6-267688 1994-10-31
JP26768894 1994-10-31
PCT/JP1995/002219 WO1996013785A1 (en) 1994-10-31 1995-10-30 Method of retrieving novel ligand compounds from three-dimensional structure database

Related Child Applications (1)

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JP2004317749A Division JP3747048B2 (ja) 1994-10-31 2004-11-01 三次元構造データベースから新規リガンド化合物を検索するためのデータベースの作成方法

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JPWO1996013785A1 JPWO1996013785A1 (ja) 1997-11-25
JP3669704B2 true JP3669704B2 (ja) 2005-07-13

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US (3) US6389378B2 (2)
EP (2) EP0790567A1 (2)
JP (1) JP3669704B2 (2)
KR (1) KR970707500A (2)
CN (1) CN1150478C (2)
WO (1) WO1996013785A1 (2)

Families Citing this family (33)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US6389378B2 (en) * 1994-10-31 2002-05-14 Akiko Itai Method of searching novel ligand compounds from three-dimensional structure database
US6549900B2 (en) 1995-12-28 2003-04-15 Akiko Itai Method for creating physiologically active compounds
EP0818744A3 (en) * 1996-07-08 1998-07-08 Proteus Molecular Design Limited Process for selecting candidate drug compounds
CA2294771A1 (en) * 1997-07-03 1999-01-14 Akiko Itai Method for inferring protein functions with the use of ligand data base
EP0918296A1 (en) * 1997-11-04 1999-05-26 Cerep Method of virtual retrieval of analogs of lead compounds by constituting potential libraries
WO2001018627A2 (en) * 1999-09-06 2001-03-15 National University Of Singapore Method and apparatus for computer automated detection of protein and nucleic acid targets of a chemical compound
US6727100B1 (en) 1999-10-21 2004-04-27 4Sc Ag Method of identifying candidate molecules
AU2002214286A1 (en) * 2000-11-15 2002-05-27 Akiko Itai Method of profiling protein
AU2001215557A1 (en) * 2000-11-30 2002-06-11 Toyo Suisan Kaisha, Ltd. Method of designing the molecular structure of inhibitor to enzyme
WO2002057954A1 (en) * 2001-01-19 2002-07-25 Mitsubishi Chemical Corporation Method of constructing three dimensional structure of protein involving induced-fit and utilization thereof
JP4179878B2 (ja) * 2001-02-02 2008-11-12 中外製薬株式会社 ペプチド誘導体
WO2003072596A2 (en) * 2002-02-27 2003-09-04 Protein Mechanics, Inc. Clustering conformational variants of molecules and methods of use thereof
US6671628B2 (en) 2002-03-04 2003-12-30 Chemnavigator, Inc. Methods for identifying a molecule that may bind to a target molecule
AU2003221884A1 (en) * 2002-04-10 2003-10-27 Transtech Pharma, Inc. System and method for data analysis, manipulation, and visualization
US20040034481A1 (en) * 2002-08-16 2004-02-19 Hurst John R. Methods for identifying a prospective binding site on a target molecule and for characterizing a site on a target molecule
WO2004022737A1 (ja) * 2002-09-03 2004-03-18 Sei-Ichi Tanuma 生理活性ペプチドの設計法及びその用途
KR100456627B1 (ko) * 2002-12-10 2004-11-10 한국전자통신연구원 3차원 구조기반의 거대분자의 기능 예측 시스템 및 그 방법
US7826979B2 (en) * 2003-02-14 2010-11-02 Vertex Pharmaceuticals Incorporated Method of modeling complex formation between a query ligan and a target molecule
JP4314128B2 (ja) * 2004-02-24 2009-08-12 株式会社インシリコサイエンス タンパク質立体構造と誘導適合を利用したリガンド探索方法
JP2005250721A (ja) * 2004-03-03 2005-09-15 Hitachi High-Technologies Corp 蛋白質または高分子複合体の検索・照合方法及び装置
US20060052943A1 (en) * 2004-07-28 2006-03-09 Karthik Ramani Architectures, queries, data stores, and interfaces for proteins and drug molecules
JP4688467B2 (ja) * 2004-10-15 2011-05-25 株式会社菱化システム 受容体−リガンド安定複合体構造探索方法
CA2600745A1 (en) * 2005-03-03 2006-09-08 The Burnham Institute For Medical Research Screening methods for protein kinase b inhibitors employing virtual docking approaches and compounds and compositions discovered thereby
JP4719223B2 (ja) * 2005-03-11 2011-07-06 シュレディンガー エルエルシー 結合親和性を推定するための予測的スコア関数
KR100839600B1 (ko) * 2006-12-04 2008-06-19 한국전자통신연구원 특이 결합부위 자동추출을 이용한 리간드 검색 장치 및 그방법
WO2008154456A2 (en) * 2007-06-06 2008-12-18 Nationwide Children's Hospital, Inc. Methods and compositions relating to viral fusion proteins
JP5052985B2 (ja) * 2007-07-31 2012-10-17 住友重機械工業株式会社 分子シミュレーション方法、分子シミュレーション装置、分子シミュレーションプログラム、及び該プログラムを記録した記録媒体
US20090124579A1 (en) * 2007-11-09 2009-05-14 University Of South Carolina Systems and Methods For Determination of Compounds for Stimulation or Inhibition of Neocalcification
EP3077823B1 (en) 2013-12-05 2019-09-04 The Broad Institute, Inc. Compositions and methods for identifying and treating cachexia or pre-cachexia
CN104750761B (zh) * 2013-12-31 2018-06-22 上海致化化学科技有限公司 分子结构数据库的建立方法及搜索方法
EP3389715A4 (en) 2015-12-14 2019-06-12 David K. Thomas COMPOSITIONS AND METHODS FOR TREATING CARDIAL DYSFUNCTION
JP7139805B2 (ja) * 2018-09-11 2022-09-21 富士通株式会社 化合物探索装置、化合物探索方法、及び化合物探索プログラム
WO2020168507A1 (zh) * 2019-02-21 2020-08-27 深圳晶泰科技有限公司 分子对接云计算流程控制方法

Family Cites Families (9)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5331573A (en) * 1990-12-14 1994-07-19 Balaji Vitukudi N Method of design of compounds that mimic conformational features of selected peptides
US5642292A (en) 1992-03-27 1997-06-24 Akiko Itai Methods for searching stable docking models of biopolymer-ligand molecule complex
JP3256307B2 (ja) 1993-01-07 2002-02-12 昭子 板井 生理活性を有するリガンドの分子構造を構築する方法
AU7311994A (en) * 1993-05-21 1994-12-20 Arris Pharmaceutical Corporation A machine-learning approach to modeling biological activity for molecular design and to modeling other characteristics
JP3785195B2 (ja) 1993-11-11 2006-06-14 昭子 板井 生理活性を有するリガンドの分子構造を構築する方法
US6389378B2 (en) * 1994-10-31 2002-05-14 Akiko Itai Method of searching novel ligand compounds from three-dimensional structure database
JP3928000B2 (ja) 1995-11-13 2007-06-13 昭子 板井 生理活性化合物の設計方法
WO1997024301A1 (en) 1995-12-28 1997-07-10 Akiko Itai Preparation method of physiologically active compound
US6389978B1 (en) * 1999-11-12 2002-05-21 Manuel B. Hooper Gun barrel cleaning shell

Also Published As

Publication number Publication date
CN1150478C (zh) 2004-05-19
WO1996013785A1 (en) 1996-05-09
EP0790567A1 (en) 1997-08-20
EP1944708A1 (en) 2008-07-16
CN1171160A (zh) 1998-01-21
US6490588B2 (en) 2002-12-03
KR970707500A (ko) 1997-12-01
US20010018682A1 (en) 2001-08-30
US20020111938A1 (en) 2002-08-15
US6389378B2 (en) 2002-05-14
EP0790567A4 (2) 1997-09-03
US20030061198A1 (en) 2003-03-27

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