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Protein structure comparison method based on contact graph

A protein structure and protein technology, which is applied in the fields of bioinformatics, intelligent optimization and computer application, can solve the problems such as optimal and the comparison efficiency needs to be further improved, and the structure comparison information cannot be guaranteed, so as to improve the efficiency and accuracy. Effect

Active Publication Date: 2019-08-13
深圳新锐基因科技有限公司
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Problems solved by technology

Since TM-align uses a heuristic iterative search, the structure alignment information obtained by it cannot be guaranteed to be optimal and the alignment efficiency needs to be further improved
[0004] In summary, the existing protein structure comparison methods are still far from the requirements of practical applications in terms of calculation cost and comparison accuracy, and urgently need to be improved.

Method used

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  • Protein structure comparison method based on contact graph
  • Protein structure comparison method based on contact graph
  • Protein structure comparison method based on contact graph

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Embodiment Construction

[0027] The present invention will be further described below in conjunction with the accompanying drawings.

[0028] refer to figure 1 and figure 2 , a method for protein structure alignment based on a contact graph, comprising the following steps:

[0029] 1) Input the three-dimensional structure information of two proteins to be compared, denoted as P a with P b ;

[0030] 2) For any two amino acid residues R from the same protein i with R j , according to their beta carbon atoms C β The three-dimensional coordinate information D i with D j , when there is no C in the amino acid residue β , the central carbon atom C α The coordinate information of C β Coordinate information, calculate their contact state m i,j : If D i with D j The distance between is less than or equal to 8 Angstroms, it means R i with R j contact, remember m i,j = 1; otherwise, it means R i with Rj no contact, remember m i,j = 0;

[0031] 3) According to step 2), calculate P a The con...

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Abstract

The invention provides a protein structure comparison method based on a contact graph. The method comprises the steps of firstly calculating contact graph information of two proteins according to three-dimensional structure information of two input to-be-compared proteins; then extracting peripheral contact information of each amino acid in the corresponding protein from a random protein contact graph; then according to the peripheral contact information of an amino acid residue, calculating a similar scoring matrix of the two proteins, wherein each element in the scoring matrix comes from similarity between the corresponding amino acids of different proteins; then according to the similar scoring matrix, acquiring comparison information of the two to-be-compared proteins by means of a dynamic planning algorithm; and finally, calculating the structure similarity score between the two to-be-compared proteins by means of a TM-score tool, and acquiring the comparison state of the proteinsin a three-dimensional space. The protein structure comparison method based on the contact graph has advantages of low calculating cost and high comparison precision.

Description

technical field [0001] The invention relates to the fields of bioinformatics, intelligent optimization and computer application, in particular to a protein structure comparison method based on a contact graph. Background technique [0002] Protein is ubiquitous and indispensable in life activities, and it undertakes a variety of biological functions in organisms. Proteins with similar structural information tend to have similar biological functions. Therefore, calculating the similarity between two different proteins by comparing their structures is helpful to the study of the biological function of the protein, and has very important guiding significance for the study of protein function and the design of drug target proteins. [0003] At present, the calculation methods specially used for protein structure alignment are: TM-align (Zhang Y, SkolnickJ. TM-align: a protein structure alignment algorithm based on the TM-score [J]. Nucleic acids research, 2005, 33( 7): 2302-23...

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Application Information

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IPC IPC(8): G16B15/00
CPCG16B15/00
Inventor 胡俊饶亮刘俊周晓根陈伟锋张贵军
Owner 深圳新锐基因科技有限公司
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