JPH0814855B2 - Protein display processing method - Google Patents

Description

DETAILED DESCRIPTION OF THE INVENTION [Outline] The present invention relates to a computer processing for displaying an image of a protein molecular structure, and an object of the invention is to provide a protein display processing method capable of easily displaying the characteristics of a structure focusing on the peptide surface of a protein molecule by relatively simple processing. Then, an image showing the molecular structure of the protein is created based on the three-dimensional coordinate data representing the relative position of each atom constituting the protein molecule, and displayed in the computer processing, for each peptide face of the protein molecule, A plane which is close to the peptide plane and includes the coordinate positions of α carbons on both sides of the peptide plane is obtained from the coordinate data by a predetermined calculation, is on the plane, and the coordinate position of the α carbons is a predetermined vertex of the diagonal line. To obtain a three-dimensional image obtained by sequentially connecting the rhombic figures to the rhombic figures of the adjacent peptide planes using the coordinates of the α carbon as connecting points. To configure.

[Industrial applications]

The present invention relates to a process for displaying an image of a protein molecular structure in a computer, and more particularly to a protein display processing method for displaying a structure focusing on a protein peptide surface.

As is known, there are many different types of proteins,
It is known that those properties are distinguished by the three-dimensional shape of the molecule, and for that purpose, three-dimensional image display of the molecular structure is used in various studies of proteins.

[Problems to be Solved by Conventional Techniques and Inventions]

The protein molecule has a molecular structure as shown in FIG. 4 (a) as well known in the art.
A portion in which C, N, and H are bonded to each other on a plane called a peptide plane is connected to ten to several thousand in sequence through a carbon atom called α carbon (denoted as Cα), and FIG. ) The shape is lined up on a complicated line as illustrated in FIG.

In that case, the respective peptide faces are oriented in various directions, and the α carbons at both ends of each peptide face are close to the peptide face, but not necessarily on the same plane.

It is said that the characteristics of various properties of various protein molecules are classified by the complicated three-dimensional structure of the molecule as described above. Therefore, three-dimensional images of molecules are used for estimating and comparing the properties of protein molecules. As shown in FIG. 5, from the data showing the three-dimensional coordinate position of each atom of various protein molecules stored in the protein database 1, the data of the designated protein is input to the display processing unit 2 and processed to obtain an appropriate data. A system that outputs a stereoscopic image to the display device 3 is used.

As a display of such a protein, there is one in which each atom is represented by a sphere in which each atom is color-coded by type. Although this is detailed, it is rather difficult to recognize the outline of the whole connection and the orientation of the peptide plane. Therefore, a ribbon-shaped graphic extending along a curve as shown in FIG. 4 (b) is also used, but the process for displaying the twist when the directions of the adjacent peptide faces are different becomes complicated. Moreover, it cannot be said that the state of each peptide surface is displayed in an easy-to-see manner.

It is an object of the present invention to provide a protein display processing method capable of easily displaying the characteristics of a structure focusing on the peptide surface of a protein molecule by a relatively simple process.

[Means for solving the problem]

 FIG. 1 is a flow chart of processing showing the configuration of the present invention.

The figure shows the flow of processing for generating and displaying an image of the molecular structure from the three-dimensional coordinate data of each atom of the protein molecule, and 10 to 14 are processing steps.

[Action]

An image showing the molecular structure of a protein is created based on the three-dimensional coordinate data representing the relative position of each atom that constitutes the protein molecule, and is displayed.
In step 10, the 3D coordinate data of the required protein molecule is read in to read the data of one carbon and the α carbons on both sides of the peptide. The plane containing is calculated by a predetermined method.

In the processing step 12, a predetermined rhombic figure which is on the plane obtained above and whose α carbon coordinate position is the apex of the diagonal line is obtained, and in the processing step 13, it is connected to the adjacent rhombic figure at the α carbon position. It is sequentially displayed and identified in processing step 14, and the above processing is repeated for all peptide surfaces.

By the above-mentioned processing method, a three-dimensional image of the protein molecular structure in which the state of the peptide surface is expressed easily can be obtained by a relatively simple processing.

〔Example〕

When creating and displaying an image showing the molecular structure of a protein based on the three-dimensional coordinate data that represents the relative positions of the atoms that make up the protein molecule, a diamond-shaped pattern that represents the peptide plane of the protein on the image display. The original form of is determined in advance and, for example, the process of FIG. 2 is started.

In processing step 20 of FIG. 2, the three-dimensional coordinate data of the required protein molecule in the protein database is read and the data of one carbon and α carbons on both sides thereof are taken out.

In processing step 21, from the coordinates of the data, the normals of the three planes determined at the positions of the three atoms, that is, the Cα-O-Cα plane, the Cα-C-Cα plane, and the Cα-N-Cα plane, are described below. And a temporary normal having the average coordinates of these three normals is calculated in processing step 22.

In processing step 23, the above-mentioned temporary normal is made a normal, and both C
A plane including the coordinates of α is determined, and a rhombic figure similar to the prototype is determined so that the coordinates of both Cα are set on the plane as the vertices of a predetermined diagonal line in the prototype of the rhombic figure.

In processing step 24, projection for displaying the rhombic figure as a three-dimensional image is performed to determine and output the coordinates of the display screen. At that time, the front and back of the peptide surface are determined according to the direction of the normal, and the display color or the shaded pattern is changed between the front and the back.

In processing step 25, it is identified whether or not the processing has been completed for all peptide surfaces of the protein molecule to be processed, and if there is unprocessing, the processing returns to processing step 20, and the data of the peptide surface adjacent to the previously extracted peptide surface is taken out, Treat as above.

Through the above processing, for example, an image of a protein molecule as shown in FIG. 3 is obtained. In the figure, the front and back of the peptide surface are distinguished by the presence or absence of a diagonal pattern.

〔The invention's effect〕

As is clear from the above description, according to the present invention, in computer processing for displaying an image of a protein molecular structure, it is possible to easily display the features of the molecular structure focused on the peptide surface of the protein molecule by relatively simple processing. There is a remarkable industrial effect that the working efficiency of the user is improved at an economical processing cost.

[Brief description of drawings]

FIG. 1 is a process flow chart showing the constitution of the present invention, FIG. 2 is a process flow chart of the embodiment of the present invention, FIG. 3 is a view showing a display example according to the present invention, and FIG. 4 is an explanatory diagram of a protein molecule. FIG. 5 is a block diagram of a configuration example of a protein display system. In the figure, 1 is a protein database, 2 is a display processing unit, 3 is a display device, 10 to 14 and 20 to 25 are processing steps.

Claims (1)

[Claims] 1. An image showing the molecular structure of a protein is prepared based on three-dimensional coordinate data representing the relative position of each atom constituting the protein molecule, and is displayed in a computer processing to display each peptide plane of the protein molecule. With respect to, the plane close to the peptide plane and including the coordinate positions of α carbons on both sides of the peptide plane is determined from the coordinate data by a predetermined calculation (1
0, 11), obtaining a predetermined rhombic figure on the plane with the coordinate position of the α carbon as the apex of the diagonal line (12), and using the rhombic figure with the coordinates of the α carbon as a connection point A protein display processing method characterized in that a three-dimensional image formed by sequentially connecting to the diamond-shaped figure on the surface is displayed (13, 14).