KR100757040B1 - System and method for analysis of interfaces based on protein domain and recording medium therefor - Google Patents

Abstract

The present invention relates to an interaction surface analysis system and method between proteins or proteins and compounds based on a protein domain, and a recording medium therefor. The interaction surface analysis system includes sequence information, chemical formula, and three-dimensional information of each analyte. And an interactive surface extraction apparatus for predicting the interactive surface between the analysis objects in three dimensions by referring to the database as the names of the interaction surface analysis objects are input or selected. An interactive surface visualization device for visually outputting the interactive surface, and the interactive surface analysis method includes inputting or selecting an analyte name, and from the database storing three-dimensional information of each analyte to the analysis object. Extract the contained atom and atom pair information to Generating, transforming each atom and pair of atoms in three dimensions, outputting each of the analytes in three-dimensional form using atoms and atom pairs depicted in three dimensions, and interacting between the three-dimensional processed analytes Predicting and visually outputting the planes allows fast and accurate extraction of the planes of interaction between protein domains or between protein domains and compounds.

Domains, proteins, compounds, interactions

Description

System and Method for Analysis of Interfaces Based on Protein Domain and Recording Medium Therefor}

1 is a block diagram of an interactive surface analysis system according to an embodiment of the present invention,

2 is a flowchart illustrating a method for analyzing an interaction surface according to the present invention;

3 is a block diagram of an interactive surface analysis system according to another embodiment of the present invention;

4 is a visualization of the interaction surface extracted from the two domains according to the analysis method of the present invention.

FIG. 5 illustrates the extraction and visualization of various interaction surfaces from various analytes using the analysis method of the present invention.

<Description of the symbols for the main parts of the drawings>

100: interactive surface analysis system 110: control unit

120: Database 122: Protein Database

124: Domain Database 126: Compound Database

130: I / O interface 140: interactive surface visualization device

142: stereoscopic information extraction unit 144: three-dimensional processing unit

146: effect processor 150: interactive surface extraction device

160: storage means 170: communication network interface

200: personal computer 300: information providing server

310: control unit 320: communication network interface

330: Database

The present invention relates to a protein interaction surface analysis system and method and a recording medium therefor, and more particularly, to a protein interaction surface analysis system and method based on a domain including a compound and a recording medium for the same.

All proteins, naturally or artificially produced, are molecules that play an important role in vivo, including structure formation, reaction catalysis, transport, regulation, and defense. Most proteins function through interactions with other molecules, especially other proteins. Indeed, protein-to-protein interactions are tightly controlled and have been significantly conserved during evolution (Bolser, D.M. et al. Genomics and Informatics, 2003, vol. 1, pp. 1-7). Unnecessary or insufficient interactions resulting from random mutations result in loss of function of the molecule. Thus, interaction domains or regions of interaction partners, particularly protein domains and ligands, have been naturally selected and significantly controlled throughout the evolution of protein interaction networks (Caffrey et al. 2004, Protein Science, vol. 13, pp 190-202).

Since 1970, efforts have been made to confirm the principle of interprotein recognition. Chothia and Janin studied the physical and chemical properties of the interaction sites of proteins involved in the recognition process (Chothia, C. et al, 1975, Nature, vol. 256, pp. 705-70). Lawrence and Colman focused on the shape complementarity of the interaction plane using the shape correlation index (Lawrence, MC et al. 1993, J. Mol. Biol. Vol. 234, pp. 946-950). . In studying the interaction planes between protein subunits and protein domains, Argos studied not only the physicochemical properties of the protein interaction planes, but also the geometrical features of the protein interaction planes (Argos, P. 1988, Protein Engineering, vol. 2). , pp. 101-113). Jones and Thornton introduced a surface patch method to identify the parameters involved in protein interactions (Jones, S. et al. 1997, Proc. Natl. Acad. Sci. Vol. 93, pp. 13-2).

As complete genomic sequences are available, interactomics of protein structures that map the interactions of all protein domains are becoming important (Kim, WK et al, 2004, Bioinformatics, vol. 20, pp. 1138-1150). Recently, the increase in experimental data, such as the yeast two hybrid, has led to the mapping of human whole protein interactants (Kim, HG et al. 2003, Lecture Notes in Computer Science, vol. 2637). , pp.159-165). Interfacial studies involving all molecules of higher resolution should now be preceded by large-scale protein interaction studies.

Korean Patent Laid-Open Publication No. 2004-0026227 relates to a technique for generating a three-dimensional graph that visualizes large-scale genome and protein-level protein interaction data. The first step of creating an initial layout by placing all of the vertical angles on the sphere surface to create an initial layout, with each node in the initial layout having a local spring force with adjacent nodes and a global with non-adjacent nodes. Efficient visualization of large-scale protein interaction data comprising a second step of generating a graph by repeating a predetermined number of times of shifting the equilibrium position in consideration of both the spring forces The technique is presented.

However, the visualization method can visualize the interaction surface of the protein in three dimensions, but it is not possible to generate three-dimensionally, and since the number of proteins known to date is about 2.3 million, it is possible to extract the interaction surface for each protein. This requires a lot of work.

The inventors have developed a system that can visualize proteins, protein domains, compounds and their interactions at high resolution. In addition, based on the fact that the function of the protein is substantially derived from the domain unit and about 65,000 domains known to date, all possible interaction surfaces are extracted and a database storing the extracted interaction surfaces is used. Ultimately, the present invention has been completed in light of the fact that a computer system can rapidly predict the interaction surface of a large number of proteins contained in a protein body with another protein or compound.

In the present invention, an "analyte" may be a protein, a protein domain, or a compound. If the analyte is a protein, it is preferable to classify it into domains and then analyze the interaction between the domain and other analytes. If all of the analytes are proteins, the interaction between proteins can be analyzed. If one is an protein and the other is a compound, the interaction between the protein and the compound can be analyzed.

In the present invention, "protein" includes about 2.3 million proteins known in the art, as well as structurally and functionally similar homologs to them.

In the present invention, "domain" refers to a functional and structural unit of a protein. In the art, domains of a protein include SCOP (Structural Classification of Protein) and FSSH (Holm L. et al. Science, 1996, vol. 273). , pp. 595-602) or CATH (Orengo, CA et al. Structure 5, pp. 1093-1108). In the present invention, it is preferable to use the domain of the database according to the SCOP.

The present invention predicts the plane of interaction between two or more different analytes. Here, the "interaction surface" is defined by an algorithm described below and means a group of atoms in contact among atoms constituting the first analysis object and atoms constituting the second analysis object. In the present invention, an Euclidean distance method, a geometric diagram (eg, Voronoi Diagram), or an accessible surface area algorithm is used to extract the interaction surface from the first and second analytes. Can be. In particular, the Euclidean distance method is based on the PSIMAP (Jong Park et al. JMB, 2001, vol. 307, pp. 929-938) method presented by the present inventors. In the following, the algorithms are described in detail.

(i) Euclidean distance method: Each atom constituting the first analyte is selected in this manner by checking whether or not interacting according to the distance with the atoms constituting the second analyte. When atoms are collected, they form an interaction surface.

(ii) geometric diagram: a point corresponding to half of the distance between atoms of each atom constituting the second analyte for each atom constituting the first analyte, which is connected to the first analyte by connecting the points; Interaction planes between the second analytes can be formed.

(iii) Approach mask algorithm: Atoms are selected for contacting the water molecules when the first analyte and the second analyte are separated, and then atoms that contact the water molecules when they are bound. A group of atoms selected from the former but not from the latter forms the interaction plane between the first analyte and the second analyte.

The present invention can visualize the interaction plane of two or more analytes using an analysis system and method described below and a recording medium therefor.

In one aspect, the present invention provides a system for analyzing an interaction surface between proteins or proteins and compounds based on a protein domain, comprising: a control unit; A database storing three-dimensional information, sequence information, and chemical formula information of each protein, domain, and compound; I / O interface; The name of at least two or more analytes (protein name, domain name, compound and protein name or compound and domain name) for which the interaction surface is to be analyzed is referred to the database as input or selected through the I / O interface. An interactive surface visualization device for displaying the analysis object in three dimensions and visualizing the interaction surface between the predicted analysis objects and visually outputting them through the I / O interface; An interaction surface extraction device for predicting an interaction surface between the analysis targets; And an interaction surface analysis system based on domains configured to include storage means.

In other respects, three-dimensional information for each analyte may be obtained as input or selection of at least two analytes (protein names, domain names, compound and protein names, or compound and domain names) for analyzing the interaction surface. Extracting atom and atom pair information included in the analyte from a database stored therein, and generating a list of atoms and atom pairs using the extracted atom and atom pair information; Modifying each atom and atom pair in three dimensions by referring to the atom and atom pair information; Arranging the atoms and atom pairs depicted in three dimensions according to three-dimensional information of the analyte, and outputting each of the analytes in a three-dimensional form; Predicting an interaction surface for the three-dimensionally processed analyte; Matching and docking respective atoms constituting the predicted interaction surface; And it provides a domain-based interaction surface analysis method comprising the step of visually outputting the predicted interaction surface through the output device.

In another aspect, the three-dimensional dimension of each analyte, as input or selection of at least two analytes (protein names, domain names, compound and protein names, or compound and domain names) for analyzing the interaction surface. Extracting atom and atom pair information included in the analyte from a database storing information, and generating a list of atoms and atom pairs using the extracted atom and atom pair information; A function of modifying each atom and atom pair in three dimensions by referring to the atom and atom pair information; Arranging the atoms and atom pairs illustrated in the three-dimensional form according to three-dimensional information of the analyte, and outputting each of the analyte in three-dimensional form; Predicting an interactive surface for the three-dimensionally processed analyte; Matching and docking respective atoms constituting the predicted interaction surface; A function of visually outputting the predicted interactive surface through an output device; And a computer readable recording medium having recorded thereon a program for sequentially executing a function of changing a visual effect of an atom or an atomic pair included in the three-dimensional processed object.

Hereinafter, exemplary embodiments of the present invention will be described in detail with reference to the accompanying drawings.

1 is a block diagram of an interactive surface analysis system according to an embodiment of the present invention.

As shown, the domain-based interaction surface analysis system 100 is a control unit 110 that controls the overall operation, such as data signal and control signal transmission and reception, sequence information of each protein, domain and compound, domain 3D At least two I / O interfaces 130 for connection between an interactive analysis system 100 and an input / output device (not shown) such as a database 120 storing information, sequence information, monitors, keyboards, mice, and the like. As the names of the two interactive surfaces analyzed are input or selected through the I / O interface 130, the database 120 is referred to in three dimensions to visualize the interactive surfaces between the predicted analysis objects. Interactive surface visualization device 140 for visually output through the I / O interface 130, for predicting the interaction surface between the analysis object It is configured to include a storage means 160 for storing the interaction surface extraction unit 150 and the interaction surface analysis information required for the operation of the system 100, between the extracted analyte interaction surface information.

Here, the name of the interactive surface analyte may be directly input by the user, or may be selected from a list of analytes such as a protein name, a domain name, or a compound name stored in the database 120, or the names of some of the analytes may be directly You can enter and select the rest of the list from the list of analysis names. To this end, the database 120 applied to the present invention is a protein DB 122 for storing protein sequence information, three-dimensional information, etc. for each protein, a domain DB for storing sequence information, three-dimensional information, etc. for each domain ( 124) and the compound DB 126 in which chemical formulas and three-dimensional information are stored for each compound.

More specifically, each database 122, 124, and 126 includes three-dimensional information of each protein, domain, and compound, and types of atoms and atom pairs included in each protein, domain, and compound. , The relative three-dimensional coordinates and diameters of atoms in each protein, domain, and compound, the distance between atoms in an atom-pair in each protein, domain, and compound, the type of bond (covalent, hydrogen, van der Waals, disulfide) Is stored.

In addition, the interactive surface visualization apparatus 140 includes a stereoscopic information extraction unit 142 and a three-dimensional processing unit 144. When the stereoscopic information extracting unit 142 inputs or selects at least two or more protein names, domain names, protein names and compound names or domain names and compound names to be analyzed through the I / O interface 130, The database 120 is queried by the control of the controller 110 to extract information on atoms and pairs of atoms constituting the respective analytes. The atomic and atomic pair information includes the relative coordinates and diameters of each atom in each of the analytes of interest, the coupling information of the two atomic pairs in the bonding relationship, and the distance between the two atoms.

When the stereoscopic information extraction unit 142 extracts atom and atom pair information on each of the corresponding analysis targets, the three-dimensional processing unit 144 generates each atom and atom pair in three-dimensional form using the atom and atom pair information. . In this case, since the relative coordinates, diameters, and atomic pairs of each atom are known, the atoms can be visualized in the form of a sphere centered on the coordinates of the atoms. We can visualize each pair of atoms in a form of two superimposed spheres.

In this way, the analysis object may be represented in three dimensions, and the interaction surface extraction apparatus 150 may describe the interaction surface with respect to the three-dimensionally processed analysis object as described above by the Euclidean distance method and the geometric method. (Eg, Voronoi diagram) or an approach mask algorithm (Accessible Surface Area) using one of the predictions. The result of the interaction plane prediction between the analysis objects is output in a three-dimensional form by the three-dimensional processing unit 144 of the interaction plane visualization apparatus 140.

In addition, the interactive surface visualization apparatus 140 according to the present invention may further include an effect processor 146. The effect processor 146 performs functions such as setting the color of the atom, the atom pair or the amino acid, setting the color according to the user's request, changing the direction, and giving an illumination effect to each atom constituting each analysis target. .

2 is a flowchart illustrating a method of analyzing an interactive surface according to the present invention.

First, a user inputs or selects at least two protein names, domain names, compound and protein names, or analyte names such as compound and domain names for analyzing an interaction surface through an input device (S110). When inputting an analysis object name, a user may directly input a user by operating a keyboard, for example, or select a desired analysis object from a list of proteins, domains or compounds stored in the database 120.

As the analysis object name is input or selected, the stereoscopic information extraction unit 142 searches the database 120 to extract atom and atom pair information included in the analysis object, and generates a list of atoms and atom pairs using the same. (S120). As described above, the atom and atom pair information includes relative three-dimensional coordinates and diameters of atoms in each analyte, distance between atoms forming atom pairs in each analyte, and bond type.

When a list of atoms and atom pairs for each analyte is generated, the three-dimensional processor 144 refers to the atom and atom pair information in three dimensions by referring to the atom and atom pair information (S130), and the three of the corresponding analytes Arranged according to the dimensional information, and as a result, each analysis object is output in a three-dimensional form (S140).

Subsequently, the interaction surface extractor 150 predicts the interaction surface for the three-dimensionally processed analyte (S150), and matches and docks the atoms constituting the predicted interaction surface, respectively. After (S160), the visual output through the output device (S170).

On the other hand, after three-dimensional processing and outputting each of the analysis target, or after outputting the predicted interaction surface, the visual effect of the atoms or pairs of atoms included in each analysis can be changed at the request of the user. That is, it can be visualized according to the needs of the operator, such as specifying different colors by atoms, atomic pairs, and amino acids, or by arbitrarily assigning colors to users, or by providing lighting effects to emphasize the interaction surface area.

In the interactive surface analysis system described above, since the database 120 is independently established for each system, it is difficult to reflect this in real time when the database 120 is changed. Therefore, if the database 120 is managed by a specific server system, and the database 120 is shared through a communication network such as the Internet, even if the database 120 is changed, it is always possible to visualize and predict the interaction surface using the latest data. It is expected to be. An interactive surface analysis system for this is shown in FIG. 3.

3 is a block diagram of an interactive surface analysis system according to another embodiment of the present invention.

The interactive surface analysis system according to the present embodiment includes a personal computer 200 equipped with the interactive surface visualization apparatus 140 and the interactive surface extraction apparatus 150, a communication network such as the personal computer 200 and the Internet 400. It includes an information providing server 300 connected through.

The personal computer 200 may be configured to connect an input / output device (not shown) such as a control unit 110, a monitor, a keyboard, a mouse, and the like to control the overall operation such as data signal and control signal transmission and reception, and the interaction analysis system 100. As the I / O interface 130 and the interactive surface analysis object name are input or selected through the I / O interface 130, the corresponding analysis object is represented in three dimensions with reference to the database 330, and the interaction between the predicted analysis objects is displayed. Interactive surface visualization device 140 for visualizing and outputting the working surface through the I / O interface 130, interaction surface extraction device 150 for predicting the interaction surface between the analysis object, interaction Storage information 160 and the Internet 400 to store information necessary for the operation of the surface analysis system 100, the interaction surface information between the extracted analysis objects, etc. It is configured to include a network interface 170 for connection to the service server 300.

Here, the interactive surface visualization device 140 includes a stereoscopic information extraction unit 142, a three-dimensional processing unit 144 and an effect processing unit 146, the function and operation of each processing unit described in Figures 1 and 2 Since it is similar to the above, a detailed description thereof will be omitted.

Meanwhile, the information providing server 300 includes a controller 310, a communication network interface 320, and a database 330. The database 330 may include a protein DB, a domain DB, and a compound DB, and include sequence information, three-dimensional information, and chemical formula information of each analyte such as each protein, domain, and compound, and atoms and atoms included in each analyte. The types of pairs, relative three-dimensional coordinates and diameters of the atoms in each analyte, the distance between atoms in the analytical pair in each analyte, and the type of bond may be stored.

In this embodiment, since the information server 300 centrally manages three-dimensional information of a protein, domain, or compound that is the basis of the interaction surface analysis, a database (if a new protein, domain, or compound is synthesized or found) The collective update of 330 is easy, and each personal computer 200 user has an advantage of using the latest three-dimensional information.

In addition, the interaction surface visualization apparatus 140 and the interaction surface extraction apparatus 150 may be configured as independent devices connected to the personal computer 140, but may be configured as one software capable of performing such a function. It is also possible. When the functions of the interactive surface visualization apparatus 140 and the interactive surface extraction apparatus 150 are manufactured by software, the information providing server 300 downloads them to the requesting user, and the user sends them to the personal computer 200. After installation, it can be used for analysis of interactive surfaces, or it can be produced in a form stored on all possible recording media such as floppy disk, CD, DVD, and the like.

4 is a visualization of the interaction surface extracted from the two domains according to the analysis method of the present invention.

After three-dimensionalizing two domains d1a25a and d1a25b classified and named by the SCOP classification system, each atom constituting the domain d125a interacts by checking the interaction with the atoms constituting the domain d1a25b. Atoms were selected, i.e., the interaction surface of domain d1a25a and domain d1a25b was extracted and visualized as white.

5 is a visualization of the various interaction surface in accordance with the analysis method of the present invention.

A three-dimensionalizes the hemoglobin protein into two domains, 1cbma_ and 1cbmb_, classified and named by the SCOP classification system, and then interacts according to the distance between the atoms constituting the domain 1cbma_ and atoms constituting the domain 1cbmb_ By checking whether or not the interaction atoms were selected, all possible interactions were extracted and visualized with dotted lines. B visualizes the three domains in the hemoglobin protein in the form of Connolly surface, radius according to van der Waals, and skeleton. C follows the same procedure as A, but visualizes the interaction surface extracted by geometric methods (eg Voronoi diagram). D is a visualization of the interaction surface extracted by the Euclidean distance method between 1 ccb, a subunit of hemoglobin protein, and the compound (Heme structure).

The three-dimensional structure and sequence of the interaction surface analyzed as described above may be used for microarray (eg, protein chip) or drug development. For example, mimics that mimic the interaction planes of domains that are frequently present in carcinogenic proteins (mimics (artificially synthesized materials similar to the three-dimensional structure of the interaction plane) are attached onto a substrate for a conventional protein chip, and then Candidates (eg, proteins, nucleic acids, compounds, etc.) that are expected to interact with the carcinogenic proteins may be injected into the candidate substances that interact with the domains.

Interaction between proteins, between domains, between proteins and compounds, or between domains and compounds using a system and method for analyzing the surface of proteins or proteins and compounds based on the protein domain according to the present invention and a recording medium therefor Surfaces can be extracted quickly and accurately at high resolution, and these analyzed surfaces can be used to predict inter-protein interaction surfaces, atomic matching and docking, drug target screening and discovery, and manufacturing of protein chips. have.

Claims (13)

A system for analyzing surface interaction between proteins or proteins and compounds based on protein domains, Control unit; A database storing three-dimensional information, sequence information, and chemical formula information of each protein, domain, and compound; I / O interface; The name of at least two or more analytes (protein name, domain name, compound and protein name or compound and domain name) for which the interaction surface is to be analyzed is referred to the database as input or selected through the I / O interface. An interactive surface visualization device for displaying the analysis object in three dimensions and visualizing the interaction surface between the predicted analysis objects and visually outputting them through the I / O interface; An interaction surface extraction device for predicting an interaction surface between the analysis targets; And Storage means; Interaction surface analysis system between proteins or proteins and compounds based on a protein domain comprising a. The method of claim 1, The database includes three-dimensional information of each protein, domain, and compound, types of atoms and pairs of atoms included in each protein, domain, and compound, relative three-dimensional coordinates and diameters of atoms in each protein, domain, and compound, each protein, and domain. And an interface between proteins or a protein-based compound based on a protein domain, characterized in that it stores distances between atoms constituting an atomic pair in the compound, binding type, sequence information of each protein and domain, and chemical formula information of each compound. Analysis system. The method of claim 1, As the interactive surface visualization apparatus inputs or selects at least two or more analysis object names to be analyzed through the I / O interface, the interactive surface visualization apparatus searches the database under the control of the control unit, and displays each of the atoms included in the analysis object. A stereoscopic information extracting unit for extracting information of atoms and pairs of atoms including relative information about the coordinates and diameters, the coupling information of two pairs of atoms in a bonding relationship, and distance information between the two atoms; And A three-dimensional processing unit for generating each atom and atom pair in a three-dimensional form using the atom and atom pair information as the atom and atom pair information included in the analysis object is extracted from the stereoscopic information extraction unit; Interaction surface analysis system between proteins or proteins and compounds based on the protein domain, characterized in that comprises a. The method of claim 3, wherein The three-dimensional processing unit visualizes each atom in the form of a sphere centered on the coordinates of the atoms, and visualizes each pair of atoms in the form of superimposing two spheres centered on the coordinates of two atoms constituting the atom pair. Characterized by the domain of a protein based protein domains or interaction surface analysis system between proteins and compounds. The method of claim 1, The apparatus for extracting the interaction surface is based on a protein domain, which predicts the interaction surface using any one or more of Euclidean distance method, geometric diagram, and accessible surface area algorithm. A system for analyzing the plane of interaction between proteins or between proteins and compounds. The method of claim 1, The interactive surface analysis system performs functions such as setting a color of each atom, atomic pair or amino acid, setting a color according to a user's request, changing a direction, and lighting effects for each atom constituting the analyte. An interaction surface analysis system between proteins or proteins and compounds based on a protein domain, characterized in that it further comprises an effect processing unit. As the names of at least two analytes (protein name, domain name, compound and protein name or compound and domain name) for analyzing the interacting surface are input or selected, three-dimensional information for each analyte is stored. Extracting atom and atom pair information included in the analyte from a database, and generating a list of atoms and atom pairs using the extracted atom and atom pair information; Modifying each atom and atom pair in three dimensions by referring to the atom and atom pair information; Arranging the atoms and atom pairs depicted in three dimensions according to three-dimensional information of the analyte, and outputting each of the analytes in a three-dimensional form; Predicting an interaction surface for the three-dimensionally processed analyte; Matching and docking respective atoms constituting the predicted interaction surface; And Visually outputting the predicted interactive surface through an output device; Method of analysis of the interaction surface between proteins or proteins and compounds based on the protein domain comprising a. The method of claim 7, wherein The atomic and atomic pair information is a protein domain-based protein between the three-dimensional coordinates and diameter of the atoms in each analyte, the distance between the atoms forming the pair of atoms in each analyte, the type of bond between proteins Or an interaction plane analysis method between a protein and a compound. The method of claim 7, wherein After the output of the analyte in the three-dimensional form, the protein between the protein domain or the protein based on the protein domain, characterized in that further comprising the step of changing the visual effect of the atoms or atomic pairs included in the analyte; Method of analysis of the interaction surface between compounds. The method of claim 9, The step of changing the visual effects of the atoms or pairs of atoms is to specify a different color for each atom, each pair of atoms, or to give a user's arbitrary color, or to give a lighting effect to highlight the interaction surface area Method of analysis of the interaction surface between proteins or between proteins and compounds based on protein domains. The method of claim 7, wherein The step of transforming each atom and the atom pair in three dimensions may visualize each atom in the form of a sphere centered on the coordinates of the atoms, and overlap two spheres centered on the coordinates of the two atoms constituting the atom pair. Visualizing each atomic pair in the form, characterized in that the protein domain based on the protein domain or the interaction surface analysis method between proteins and compounds. The method of claim 7, wherein Predicting the interaction plane for the analyte includes predicting the interaction plane using any one or more of Euclidean distance method, geometric diagram, and accessible surface area algorithm. Method for analyzing the surface of the protein-based or the interaction between the protein and the compound based on the protein domain, characterized in that. As the names of at least two analytes (protein name, domain name, compound and protein name or compound and domain name) for analyzing the interacting surface are input or selected, three-dimensional information for each analyte is stored. Extracting atom and atom pair information included in the analyte from a database and generating a list of atoms and atom pairs using the extracted atom and atom pair information; A function of modifying each atom and atom pair in three dimensions by referring to the atom and atom pair information; Arranging the atoms and atom pairs illustrated in the three-dimensional form according to three-dimensional information of the analyte, and outputting each of the analyte in three-dimensional form; Predicting an interactive surface for the three-dimensionally processed analyte; Matching and docking respective atoms constituting the predicted interaction surface; A function of visually outputting the predicted interactive surface through an output device; And Changing the visual effect of atoms or pairs of atoms included in the three-dimensionally processed analyte; A computer-readable recording medium having a program recorded thereon for executing the program sequentially.

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