JP2000222421A - Protein analysis aiding device and storage medium storing program for allowing computer to execute processing in the device - Google Patents

Abstract

PROBLEM TO BE SOLVED: To provide a protein analysis aiding device capable of extracting the amino acid residual group parts of a protein interacting with a low molecular weight compound in a form of including much information related to the structure of the protein. SOLUTION: The protein analysis aiding device retrieves amino acid residual groups including respective atoms of a specified kind in a specified compound and atoms of the specified kind in the specified protein included in a prescribed distance range by using information stored in a protein data base(PDB), generates an arrayed pattern by arraying respective amino acid residual groups obtained as retrieved results in the order of the primary array of amino acid residual groups constituting the specified protein and obtains the array pattern as information expressing the primary array structure of parts including the amino acid residual group parts of the protein interacting with the specified compound.

Description

DETAILED DESCRIPTION OF THE INVENTION

[0001]

BACKGROUND OF THE INVENTION 1. Field of the Invention The present invention relates to a protein analysis support apparatus for obtaining useful information for analyzing the properties of a protein, and more particularly, to a low molecular weight compound from a sequence of amino acid residues describing a primary sequence of a protein. The present invention relates to a protein analysis support apparatus for extracting a sequence pattern of amino acid residues constituting a portion expected to interact with a protein.

[0002] The present invention also relates to a storage medium storing a program storing a program for causing a computer to perform the processing in the protein analysis support apparatus as described above.

[0003]

2. Description of the Related Art Predicting a protein that interacts with a low-molecular compound can predict the protein (enzyme) required to change the low-molecular compound (substrate). It is important in the field. A database describing the three-dimensional structure of a protein and its low molecular weight compounds that are entangled with the complexly folded filamentous protein (eg, PDB:
Protein Data Bank).

Conventionally, using such a database,
An apparatus has been proposed which searches for an amino acid residue sequence of a protein that interacts (binds) with a low molecular compound (binding substance) (JP-A-7-056931). In this conventional device,
When a protein and a low-molecular compound are specified, the amino acid residue sequence of the protein within a predetermined distance from each element of the low-molecular compound is converted to the low-molecular compound based on the three-dimensional structural data of the specified protein and the low-molecular compound described in the database. It is extracted as a binding site with the compound.

[0005]

For example, as shown in FIG. 1, protein P has a complicatedly bent structure in the form of a thread. The amino acid residue portions C1 and C2 of the protein P that are close to each other (within a predetermined distance) are discretely present in the amino acid residue sequence in the primary sequence. Therefore, in the above-mentioned conventional apparatus, only the amino acid residue sequences C1 and C2 extracted as the binding site can be obtained individually.

[0006] The properties of a protein depend on its three-dimensional structure. Only the amino acid residue sequences C1 and C2 individually extracted as described above, the sequence order of the amino acid residue sequences C1 and C2, and the like. The conditions during that period are unknown, and are not sufficiently useful information for analyzing the properties of proteins that depend on three-dimensional structures. That is, in the protein described by the primary sequence of the amino acid residues, the amino acid residue sequences C1, C2 individually extracted exist in the order of C1, C2, or exist in the order of C2, C1. Or
Alternatively, information such as conditions under C1 and C2 is unknown.

Accordingly, a first object of the present invention is to provide a protein analysis support apparatus capable of extracting an amino acid residue portion of a protein interacting with a low molecular compound in a form containing more information on the structure of the protein. To provide. A second object of the present invention is to provide a storage medium storing a program for causing a computer to perform the above-described processing in the protein analysis support device.

[0008]

In order to solve the first problem, the present invention, as described in claim 1, describes three-dimensional structural data of a protein and a compound existing in the vicinity of the protein. A protein analysis support device for obtaining information on amino acid residue portions of a specified protein that is predicted to interact with a specified compound by using the specified database, each atom of a specified type in the specified compound Search means for searching for amino acid residues containing a specified type of atom in a specified protein existing within a predetermined distance range using the information of the database; and each of the search results obtained by the search means. The amino acid residues are arranged in the order of the primary sequence of the amino acid residues constituting the designated protein according to a predetermined notation rule, and are patterned. Sequence pattern generating means for generating a sequence pattern, wherein the sequence pattern is obtained as information representing a primary sequence structure of a portion including an amino acid residue portion of a protein interacting with a designated compound. .

In such a protein analysis support apparatus,
Each amino acid residue obtained as a search result is arranged and patterned in the order of the primary sequence of the amino acid residue constituting the designated protein according to a predetermined notation rule. Therefore, the sequence pattern obtained as a result of this patterning is expressed as an integrated sequence pattern even if the obtained amino acid residues are discrete according to the order of the primary sequence. As a result, from this sequence pattern, the sequence order of the discrete amino acid residues and the approximate primary sequence structure of the residue portion of the protein including the portion that interacts with the compound can be grasped.

The above-mentioned predetermined notation rule is not particularly limited, but satisfies the requirements (easiness of display, simplicity of array pattern search algorithm, etc.) in a system using information of the generated array pattern. Is preferred. From the viewpoint that an array pattern described in a simpler manner can be obtained, in the present invention, as described in claim 2,
The sequence pattern generation means arranges the amino acid residues represented by one letter in the order of the primary sequence of the amino acid residues constituting the designated protein, and the amino acid residues discretely present in the order of the primary sequence. It can be configured to generate array pattern information by inserting a predetermined pattern notation between them.

In such a protein analysis support device,
A sequence pattern in which letters representing amino acid residues and a predetermined pattern notation are successively arranged in the order of the primary sequence of the amino acid residues constituting the protein is obtained. The database may be provided in the protein analysis support apparatus, or may be obtained from an external communication network such as the Internet. When the information is obtained from an external communication network, all the information in the database can be downloaded into the apparatus, or can be used with a communication line connected.

[0012] In order to analyze the properties of a newly discovered protein, the generated sequence pattern is derived from the amino acid residue sequence constituting the new protein by the amino acid residues represented by the generated sequence pattern. It can be used in a system that searches columns. Also, the generated sequence pattern can be simply displayed and used by researchers or the like.

[0013] From the viewpoint of providing a protein analysis support apparatus having a function of displaying a generated sequence pattern by providing a database in the apparatus as described above, the present invention provides a method as described in claim 3. Using a database that describes the three-dimensional structural data of a protein and compounds present in the vicinity of the protein, to obtain information on the amino acid residue portion of the specified protein that is predicted to interact with the specified compound In the protein analysis support apparatus, a database storage means for storing the database, and an amino acid containing an atom of a specified type in a specified protein existing within a predetermined distance from each atom of a specified type in a specified compound Search for searching for residues using information in the database read from the storage means And generating a sequence pattern in which the amino acid residues obtained as a result of the search by the search means are arranged in the order of the primary sequence of the amino acid residues constituting the designated protein according to a predetermined notation rule, and are patterned. And a display means for displaying the sequence pattern as information representing a primary sequence structure of a portion including an amino acid residue portion of a protein interacting with a designated compound.

In order to solve the second problem of the present invention,
As described in claim 4, the present invention uses a database describing three-dimensional structural data of a protein and a compound present in the vicinity of the protein, and specifies a designated compound predicted to interact with the designated compound. In a storage medium storing a program for causing a computer to perform processing in a protein analysis support device for obtaining information on amino acid residue portions of a protein, each atom of a specified type in a specified compound and a predetermined distance A search procedure for searching for an amino acid residue containing an atom of a specified type in a specified protein existing in a range using information of the database, and each amino acid residue obtained as a search result by the search means. Are arranged in the order of the primary sequence of amino acid residues constituting the designated protein according to a predetermined notation rule. A sequence pattern generating procedure for generating a turned sequence pattern, wherein the sequence pattern is obtained as information representing a primary sequence structure of a portion including an amino acid residue portion of a protein interacting with a designated compound. It is configured as a storage medium storing a program.

The storage medium is not particularly limited as long as the program can be read out by a computer. A medium such as a CD-ROM for optically reading a program written mechanically, a magnetic medium for reading out a program, etc. Use a medium such as a magnetic disk for reading and writing the program, a medium such as a semiconductor memory for electrically reading and writing the program, and a medium such as a magneto-optical disk for reading and writing the program using light and magnetism. be able to.

[0016]

DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS One embodiment of the present invention will be described below with reference to the drawings. A basic configuration of a system to which a protein analysis support device according to an embodiment of the present invention is applied is, for example, as shown in FIG. In FIG. 2, this system is a so-called client-server system, and includes a plurality of client terminals 10, 11, 1 and 2.
2 and the server 20 are connected by a LAN. The server 20 has a database (PDB) that describes the three-dimensional structure of a protein and a low-molecular compound contained in a thread-like chain of the protein. Each client terminal 10,
The server 11 and the server 20 are configured by a general computer system, for example, as illustrated in FIG.

In FIG. 3, the computer system includes a CPU 101, a memory unit 102, a LAN unit 103, an input unit 104, a display unit 10
5, a CD-ROM drive unit 106 and an auxiliary storage device (for example, a disk device) 107. Each unit is connected by a bus B. CPU 101
Controls the entire system according to a program stored in the memory unit 102 and executes a protein analysis process as described later. Memory unit 10
Reference numeral 2 includes a ROM and a RAM, and stores programs to be executed by the CPU 10 and a table and a CPU 1.
01 is stored. LAN
The unit 103 controls data communication between the client and the server via the LAN.

The input unit 104 has a mouse and a keyboard, and is used by a user to input necessary information to the system. The display unit 105 displays data necessary for the above-described protein analysis processing, the analysis result thereof, and the like. The CD-ROM drive unit 106 reads information from the set CD-ROM 200. According to the control by the CPU 101, the CD-R
The programs and databases stored in the OM 200
The data is read by the CD-ROM drive unit 106 and stored in the auxiliary storage device 107. Auxiliary storage device 1
The program stored in 07 is transferred to the memory unit 102 when the system is started, and the CPU 101 executes processing according to the program stored in the memory unit 102. In particular, in the server 20, the P
DB (Protein Data Bank) is, for example, CD-ROM2
00, and the PDB is stored in the auxiliary storage device 107. Note that this PDB can be provided to the server 20 via an external communication network such as the Internet, for example.

In the PDB, for example, information as shown in FIGS. 4 and 5 is registered in advance. FIG. 4 shows information on the protein (ATOM row). That is, the name of each amino acid residue (MET, THR, GLU (above, three-letter notation), etc.) constituting the protein, the atoms constituting the amino acid residue, the three-dimensional position coordinates (three-dimensional structure) of each atom, and An ID name for identifying a protein is registered. FIG.
As shown in FIG. 1, information on low molecular weight compounds known to be present in the filamentous chain of protein P (HETA
TOM line). That is, a compound name (such as GNP (three-letter notation)), atoms constituting the compound, three-dimensional position coordinates (three-dimensional structure) of each atom, an ID name for specifying the low-molecular compound, and the like are registered. .

When the user operates, for example, the client terminal 10
In the case of performing protein analysis using, the CPU 101 of the client terminal 10 executes processing according to the procedure shown in FIG. In FIG. 6, the user operates the input unit 10.
When a start operation of the analysis process is performed in step 4, a PDB reading process is performed (S1). In the PDB reading process, first, a request for the PDB is made to the server 20 via the LAN unit 103 and the LAN. As a response, when the PDB is returned from the server 20 and received by the LAN unit 103, the PDB is stored in the auxiliary storage device 1.
07 is stored.

When the PDB is connected to the client terminal 10 in this manner,
Is read, the names of the proteins and low-molecular compounds described in the PDB (see FIGS. 4 and 5) are displayed on the display unit 1.
05 is displayed. Then, when the user specifies the target protein and low-molecular compound from the displayed proteins and low-molecular compounds by operating the input unit 104, the specified protein and low-molecular compound are obtained (S2). When the CPU 101 obtains a protein and a low-molecular compound specified by the user, a list of the atomic species constituting them is displayed on the display unit 105.

When the user designates the atomic species of the low-molecular compound to be examined for the presence or absence of the interaction by operating the input unit 104 from the atomic species constituting each of the protein and the low-molecular compound, and designates the atomic species of the protein, Those atomic species pairs are obtained (S3, S4). Then, when the user specifies the range of the interatomic distance predicted to interact with the input unit 104, the range of the interatomic distance is obtained (S5).

As described above, when the atomic species and the range of the interatomic distance of the protein and the low molecular weight compound are obtained, a search condition is created and registered based on the information (the memory condition of the memory unit 102). (Stored in a predetermined area) (S6). This search condition is, for example, a protein low molecular weight compound The range of interatomic distance C (carbon) O (oxygen) 3.5 ° or less. That is, in this case, the search condition is “the carbon atom C of the protein whose distance to the oxygen atom O of the low molecular compound is 3.5 ° or less”.

It is determined whether or not the end operation of the search condition setting process has been performed by the user (S7). If the end operation has not been performed yet, the above-described processes (S3, S4, S5, S6) is repeatedly executed, and the search conditions described in the range of each atomic type and interatomic distance of the protein and the low-molecular compound as described above are sequentially registered.

When the search condition setting process is terminated, a condition file describing each search condition is read out from the memory unit 102, and the condition file
The data is transmitted to the server 20 via the AN (S8). Then, the CPU 101 of the client terminal 10 waits for a response from the server 20 (S9). When the server 20 receives the condition file transmitted from the client terminal 10 as described above, the CPU 1 of the server 20
01 executes a process according to the procedure of FIG. 7, for example.

In FIG. 7, the condition file described above is
When the condition file is received by the AN unit 103 (S21), the condition file is expanded in the memory unit 102. In this state, by referring to the condition file, first, the first condition (atomic species pair, range of interatomic distance) is acquired (S
22). When the conditions are acquired in this manner, the low-molecular-weight compounds and proteins of interest are referred to the PDB stored in the auxiliary storage device 107 (see FIGS. The atoms of the molecular compound and the protein, and the amino acid residue to which the atom of the protein belongs are specified (S23). This process, for example,
This is done as follows.

First, an atom (for example, O1) belonging to an atomic species (for example, oxygen atom O) of a low molecular compound serving as a search condition
A, O2 *, O2B,...) Are all extracted, and atoms (for example, CA, CB, CE,...) Belonging to a protein atom type (for example, carbon atom C) serving as a search condition.
・ ・) Are all extracted. Then, the distance from each of the extracted atoms of the low molecular compound to each of the extracted atoms of the protein is calculated using the three-dimensional position coordinate data of each of the atoms in the PDB. Then, an atom pair that satisfies the condition of the range of the interatomic distance in the search condition (for example, 3.5 ° or less) is specified, and the interatomic distance is specified. Then, an amino acid residue containing an atom of one of the paired proteins is specified.

As described above, when an atom pair or the like satisfying the search condition is extracted, it is determined whether or not the received condition file still includes the search condition (S24). In this case, the above processing (S22, S23) is executed for the next search condition. Thereafter, the same processing is repeatedly executed for all the search conditions included in the received condition file.

When the processing for all the search conditions included in the received condition file is completed, a file of the result is created (S25). In this file, for example, as shown in FIG. 8, the interatomic distance of the extracted atom pair, the atom of one protein of the atom pair, the amino acid residue containing the atom, the residue number, and the other of the atom pair Are described. Then, based on the content of the file created as described above, the sequence pattern of amino acid residues including the atoms of the protein predicted to interact with the designated atoms of the low-molecular compound is generated as a motif pattern (S26). ).

The motif pattern is generated as follows. For example, when the extraction result as shown in FIG. 8 is obtained, the amino acid residues are represented by one letter, and the amino acid residues are arranged in the order of the residue numbers. GKSA... F.D..T become that way. This corresponds to residue numbers (16) to (18)
Amino acid residue sequence "GKSA" which is continuously arranged up to
And amino acid residue F located at residue number (28), amino acid residue D located at residue number (30), and amino acid residue T located at residue number (35) are sequentially arranged. It represents that.

Here, the amino acid residue between residue numbers (18) and (28) does not contain carbon C which is expected to interact with oxygen O of low molecular weight compounds. Therefore, the condition between the amino acid residue A (residue number (18)) and the amino acid residue F (residue number (28)) is changed, for example, by connecting “.” And “*” to “. *”. Is described. “.” Defines the presence of any amino acid residue, and “*” defines repeat. Therefore, ". *" Means that an arbitrary amino acid residue (character) is arranged at an arbitrary length. By using the symbols “.” And “*” thus defined, the amino acid residue F (residue number (2
8)) and D (residue number (30)) and amino acid residues D (residue number (30)) and F (residue number (3
5)) can also be expressed by “. *”, Respectively. As a result, the amino acid residue sequence “GKSA... F... D... F” extracted as described above becomes “GKSA.
* F. * D. * F "is described as an amino acid residue sequence pattern (motif pattern).

This motif pattern is composed of “a continuous amino acid residue sequence GKSA, an arbitrary number of arbitrary amino acid residue sequences, an amino acid residue F, an arbitrary number of arbitrary amino acid residue sequences, an amino acid residue D, an arbitrary number of amino acid residues D, An arbitrary amino acid residue sequence and an amino acid residue T are sequentially arranged. " That is, this motif pattern is based on the sequence order of amino acid residues G, K, S, A, F, D, and F, the continuity of amino acid residues, and the condition between discrete amino acid residues. Each piece of information will be included.

When the motif pattern is generated as described above, the motif pattern is transmitted from the LAN unit 103 to the LAN together with the extraction result file (see FIG. 8).
(S27). A series of processes in the server 20 ends here. Returning to FIG. 6, the CPU 101 of the client 10 that has been waiting for a response from the server 20 transmits the extracted result file and the motif pattern from the server 20 to the LAN unit 1.
When it is determined that the received information has been received at step 03, display processing of the received information is performed (S10). In this display processing, the content of the extraction result file (see FIG. 8) and the motif pattern (for example, “GKSA. * F. * D. * F”)
Is displayed in a predetermined window of the display unit 105.

The user can visually confirm, for example, whether or not the motif pattern is present in a new protein whose primary sequence of amino acid residues has been obtained by analysis. If such a motif pattern is present, it can be predicted that this new protein will also interact with the low molecular weight compound specified above. In the above example, the processing for obtaining the motif pattern is performed in a distributed manner between the client and the server. However, the processing can be performed only on the client side (stand-alone).
In this case, the PDB may be received from the server, or may be directly provided to the client by a CD-ROM or the like.

When the PDB is provided on the client side and the condition file is transmitted from the client to the server (S6 in FIG. 6), information on the specified low-molecular compound and protein described in the PDB (including the three-dimensional structure) is included. ) Can be sent to the server. In this case, the server extracts an amino acid residue or the like that satisfies the search condition from the received information on the low-molecular compound and the protein.

In the above example, the processing result was obtained under one search condition (the range of the distance between atoms and the pairs of proteins and low-molecular compounds) (see FIG. 8). Is a superposition of the processing results under each search condition. Furthermore, for example, according to the character string search system disclosed in Japanese Patent Application No. 10-109139 filed by the present applicant, the motif pattern as described above is automatically obtained from the amino acid residue sequence of a new protein. You can also search for

In the character string search processing executed by the already applied character string search system, for example, a sequence condition of a character representing an amino acid residue can be designated according to the following rules (1) to (8). . (1) Specification of specific character Description example: A Meaning: Specify character A (2) Specification of multiple characters Description example: [ABC] Meaning: Specification of any character of A, B, C (3) Specification Specification of a character different from the character of example Description example: [@A] Meaning: Specification of a character other than A (4) Specification of an arbitrary character (anything is acceptable) Example of description: Meaning: Specification of any character (5) Specification of repetition Description example: * Meaning: Repeat the previous pattern (character) 0 or more times (6) Specification of repetition of the specified number of times Description example: \ {3 \} Meaning: Immediately Repeat the pattern (character) three times (7) Specify the repetition of the specified number of times Example: \ {3,5 \} Meaning: Repeat the previous pattern (character) three to five times (8) Multiple character strings Example of description: (XXX | YYY | XXX) Meaning: Specification of any character string of XXX, YYY, ZZZ When specifying a character string in accordance with the above rules (array conditions), a search that describes search conditions For example, the following character strings can be specified by the condition information.

By inputting search condition information "ABCDE" in accordance with the above rule 1), the character string "ABDE" is entered.
“CDE” is specified. By inputting search condition information “AB [CDE] FG” in accordance with the above rules 1) and 2), character strings “ABCFG”, “ABDF”
G "and" ABEFG "are designated.

According to the above rules 1) and 3), "ABC
By inputting the search condition information “[D] E”, the character strings “ABCAE”, “ABCBE”, “ABC
CE "," ABCEC ",... Are designated. By inputting search condition information “AB.CD” according to the above rules 1) and 4), the character string “ABAC” is input.
D "," ABBCD "," ABCCD "," ABDC "
D ",... Are designated.

According to the above rules 1) and 5), "AB *
By inputting the search condition information “CD”, the character strings “ACD”, “ABCD”, “ABBCD”, “A
BBBCD ",... Are designated. Rule 1) above,
According to 4) and 5), by inputting search condition information “AB. * CD”, the character string “ABCD”,
“ABXCD”, “ABXYZCD”,... Are designated.

According to the above rules 1) and 6), "AB \
The character string "ABBBBBCD" is specified by inputting search condition information "$ 4 \ $ CD". According to the above rules 1) and 7), by inputting search condition information “AB \\ 2,4 \｝ CD”, the character string “AB
"BCD", "ABBBCD", and "ABBBBBCD" are designated.

According to the above rules 1) and 8), "AB
(CDE | F) GH ", the character strings" ABCDEGH "," ABFGGH "
Is specified. When generating a motif pattern as information to be input to the character string search system as described above, focus on various regularities at amino acid residue portions that are predicted to interact with individually extracted low-molecular compounds. Then, an integrated motif pattern can be generated.

In the above example, step S in FIG.
The processing in 22 to S25 corresponds to the search means, and the processing in step S26 corresponds to the array pattern generating means. Further, the auxiliary storage device 107 corresponds to a database storage unit, and the processing and display unit 105 in step S10 in FIG. 10 corresponds to a display unit.

[0044]

As described above, according to the present invention as set forth in claims 1 to 3, the sequence pattern obtained as a result of the patterning is such that the obtained amino acid residue is the same as that of the primary sequence. It is expressed as an integrated sequence pattern even if it is discrete according to the order, and from that sequence pattern, the sequence order of the discrete amino acid residues and the rough primary sequence of the protein residue part including the part that interacts with the compound For example, the amino acid residue portion of a protein that interacts with a low-molecular compound can be extracted in a form that contains more information on the structure of the protein, for example, the structure can be grasped.

According to the invention of claim 4,
It is possible to provide a storage medium storing a program for causing a computer to perform the above-described processing in the protein analysis support apparatus.

[Brief description of the drawings]

FIG. 1 is a diagram showing an example of the relationship between a protein and a low molecular weight compound present in the vicinity thereof.

FIG. 2 is a block diagram showing an example of a system to which the protein analysis support device according to one embodiment of the present invention is applied.

FIG. 3 is a block diagram showing a basic configuration example of each client and server shown in FIG. 2;

FIG. 4 is a diagram showing an example of information on a protein registered in a PDB.

FIG. 5 is a diagram showing an example of information on a compound registered in a PDB.

FIG. 6 is a flowchart illustrating a procedure of a process for creating a condition file executed by the client terminal.

FIG. 7 is a flowchart illustrating a procedure of a process for creating a motif pattern executed by the server.

FIG. 8 is a diagram illustrating an example of information extracted according to a search condition.

[Explanation of symbols]

 10, 11, 12 Client terminal 20 Server 101 CPU 102 Memory unit 103 LAN unit 104 Input unit 105 Display unit 106 CD-ROM drive unit 107 Auxiliary storage device 200 CD-ROM

 ────────────────────────────────────────────────── ─── Continuation of the front page (72) Inventor Norihiro Oya 2-2-1 Momodohama, Sawara-ku, Fukuoka, Fukuoka Prefecture F-term in the Fujitsu Kyushu System Engineering Co., Ltd. (Reference) 2G045 AA34 DA36 JA01 JA04 JA05 JA07 5B075 ND04 NK39

Claims (4)

[Claims] 1. Using a database describing the three-dimensional structural data of a protein and a compound present in the vicinity of the protein, information on the amino acid residue portion of the specified protein predicted to interact with the specified compound In the protein analysis support apparatus for obtaining, the specified type of atoms in the specified compound and the amino acid residues containing the specified type of atoms in the specified protein existing within a predetermined distance range from the database A search means for searching using information, and arranging each amino acid residue obtained as a search result by the search means in the order of the primary sequence of amino acid residues constituting the designated protein according to a predetermined notation rule Array pattern generating means for generating a patterned array pattern; Protein analysis support apparatus that obtained as information representing the primary sequence structure of a portion including a portion of amino acid residues of the compound and the interacting proteins. 2. The protein analysis support device according to claim 1, wherein the sequence pattern generating means arranges the amino acid residues represented by one letter in the order of the primary sequence of the amino acid residues constituting the designated protein. In addition, a protein analysis support device that generates a sequence pattern information by inserting a predetermined pattern notation between amino acid residues that are discretely present in the order of the primary sequence. 3. Using a database describing three-dimensional structural data of a protein and a compound existing in the vicinity of the protein, information on amino acid residue portions of the specified protein which are predicted to interact with the specified compound. A database storage means for storing the database; and a specified type of a specified protein existing within a predetermined distance from each atom of the specified type in the specified compound. Searching means for searching for amino acid residues containing atoms using the information of the database read from the storage means, and specifying each amino acid residue obtained as a search result by the searching means in accordance with a predetermined notation rule Of amino acid residues composing the protein sequence Protein analysis support having sequence pattern generating means for generating a pattern, and display means for displaying the sequence pattern as information representing a primary sequence structure of a portion including an amino acid residue portion of a protein interacting with a designated compound apparatus. 4. Use of a database describing the three-dimensional structure data of a protein and a compound existing in the vicinity of the protein to obtain information on amino acid residue portions of the specified protein which are predicted to interact with the specified compound. In a storage medium storing a program for causing a computer to perform a process in a protein analysis support apparatus for obtaining a specified protein existing within a predetermined distance from each atom of a specified type in a specified compound A search procedure for searching for an amino acid residue containing the atom of the type specified in the above-mentioned database using the information of the database; and specifying each amino acid residue obtained as a search result by the search means in accordance with a predetermined notation rule. Sequence pattern patterned by arranging in the order of the primary sequence of the amino acid residues constituting the protein And storing a program for obtaining the sequence pattern as information representing a primary sequence structure of a portion including an amino acid residue portion of a protein interacting with a designated compound. Medium.