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Prediction method for protein three-dimensional structure

A three-dimensional structure and protein technology, applied in special data processing applications, instruments, electrical digital data processing, etc., can solve the problems of low prediction accuracy of protein structure, large amount of calculation, difficult placement of amino acid side chains, etc., to achieve the solution of side chain The effect of placement problem, small amount of calculation, and fast calculation speed

Inactive Publication Date: 2008-10-29
THE INST OF BASIC MEDICAL SCI OF CHINESE ACAD OF MEDICAL SCI
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Problems solved by technology

[0007] In order to overcome the shortcomings of low protein structure prediction accuracy, difficult placement of amino acid side chains, and huge amount of calculation in the prior art, the purpose of the present invention is to provide a method for predicting the three-dimensional structure of proteins with fast calculation speed and high precision

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  • Prediction method for protein three-dimensional structure
  • Prediction method for protein three-dimensional structure
  • Prediction method for protein three-dimensional structure

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Embodiment

[0033] Taking a small protein fragment as an example, a specific implementation method is introduced. Suppose you want to predict the 3D structure of the segment "SGLFDFLKRKEVKE".

[0034] First, assuming the three-dimensional coordinates of the starting amino acid "S", it can be set as (generally, the coordinates of the skeleton atoms of a random residue in the crystal structure can be used):

[0035] N = (41.272, 7.927, -56.483);

[0036] Cα = (40.571, 9.126, -55.942);

[0037] C=(41.440, 10.386, -55.943);

[0038] O=(41.256, 11.281, -55.115);

[0039] When setting the coordinates of the starting amino acid, the relative position of each atom must conform to the inherent law of amino acids.

[0040] Then, with the second amino acid "G" as the center, a fragment of nine amino acids long is intercepted in the sequence, and the deficiency is filled with spaces to obtain "---SGLFDF" ("-" indicates a space).

[0041] Then search for the fragment with the highest degree of si...

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Abstract

The invention provides a method for predicting three dimensional structure of protein; the method comprises the following steps: (1) an amino acid (for example the first one) in the object protein sequence of the three dimensional structure to be predicted is used for setting a predicted coordinate value; (2) next amino acid (for example the second one) in the (1) is taken as the center amino acid and divides a nonpeptide fragment in the object sequence; (3) the nonpeptide fragment which is matched perfectly with the sequence in the step (2) is searched in the nonpeptide fragment data base; (4) the coordinate of the center amino acid of the object nonpeptide fragment is calculated according to the corresponding coordinate of the center amino acid of the searched best matching fragment and is assembled to the object protein; (5) next amino acid (for example the third one) is taken as next center amino acid and carries out the steps of division, searching and assembling till the final amino acid is assembled completely; the object protein sequence structure obtained through the method of the invention has the advantages of better preciseness, little operation and fast calculation, solves the problem of arrangement of a side chain.

Description

technical field [0001] The invention belongs to the field of ab initio prediction (Ab Initio) of protein three-dimensional structure prediction methods, in particular to a protein structure prediction method based on central amino acid assembly of polypeptide fragments. Background technique [0002] With the completion of the Human Genome Project, we have entered the era of the proteome. The main task of the proteome project is to understand each protein, which includes the sequence, structure and function of each protein. For any protein, the sequence determines its structure, and it is this unique structure that gives it a unique function. Therefore, obtaining the three-dimensional structure of a protein is of great significance for understanding its function. At present, some experimental methods (X-ray crystallography, nuclear magnetic resonance, etc.) can be used to obtain the spatial structure of a protein. However, these experimental methods have their own limitati...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G01N35/00G06F19/00G06F19/16
Inventor 唐鹤云张正国杨啸林郭亚峰
Owner THE INST OF BASIC MEDICAL SCI OF CHINESE ACAD OF MEDICAL SCI
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