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Track multiscale analysis method used for protein structure prediction

A multi-scale analysis and protein structure technology, applied in the field of computer applications and bioinformatics, can solve the problems of inability to display and accurately capture small structural differences, and achieve the effect of accurate capture

Inactive Publication Date: 2017-09-08
ZHEJIANG UNIV OF TECH
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Problems solved by technology

[0004] In order to overcome the shortcomings of the existing conformational space search trajectory analysis methods that cannot accurately capture small structural differences and cannot display structural composition methods such as folding types and contact modes, the present invention proposes a trajectory multi-scale analysis method for protein structure prediction

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  • Track multiscale analysis method used for protein structure prediction
  • Track multiscale analysis method used for protein structure prediction
  • Track multiscale analysis method used for protein structure prediction

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Embodiment Construction

[0035] The present invention will be further described below in conjunction with the accompanying drawings.

[0036] refer to Figure 1 ~ Figure 3 , a trajectory multi-scale analysis method for protein structure prediction, the method comprising the following steps:

[0037] 1) PDB files of all conformations in a given search trajectory;

[0038] 2) Set the distance threshold K;

[0039] 3) Obtain the binary association map of all conformations:

[0040] 3.1) read the PDB file, let i=1, i is the amino acid residue sequence number in the protein PDB file;

[0041] 3.2) Read the coordinate information Cor_i of the i-th residue;

[0042] 3.3) Calculate the Euclidean distance Dij between the i-th residue and the j-th residue, j∈(i+1,l), where l is the length of the protein sequence;

[0043] 3.4) Judge the relationship between Dij and K;

[0044] 3.5) If Dij>K, then record 0 at the position of the i-th row j column of the binary correlation diagram;

[0045] 3.6) If Dij

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Abstract

The invention discloses a track multiscale analysis method used for protein structure prediction. A binary association graph is adopted for representing global folding information of protein conformations; structure difference among different conformations is represented with a Hamming distance; by constructing a global difference information matrix of a search track, the difference information matrix is converted into a two-dimensional plane structure difference information graph by adopting a multidimensional scale analysis method; and through the plane structure difference information graph, a structure relationship of all the conformations in a search process can be obtained, and tracking and viewing of the search track are realized. The method is applied to the protein structure prediction; and by analyzing the search track, tiny structure difference can be accurately captured and information of structural composition modes such as a folding type, a contact mode and the like can be displayed.

Description

technical field [0001] The invention relates to the fields of bioinformatics and computer applications, in particular to a trajectory multi-scale analysis method for protein structure prediction. Background technique [0002] Bioinformatics is a research hotspot in the intersection of life science and computer science. Ab initio prediction of protein structure is an extremely important research problem in bioinformatics. In the problem of protein structure ab initio prediction, it is necessary to analyze the trajectory of the prediction method in the conformational space to obtain useful information to guide the algorithm. Optimization, and then a preliminary evaluation of the prediction method to screen out the optimized conformation with a reasonable structure. The protein conformation trajectory data obtained by performing a search process is high-dimensional, that is to say, the protein has a large number of residues, and each residue has its corresponding parameter dat...

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Application Information

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IPC IPC(8): G06F19/16
CPCG16B15/00
Inventor 张贵军郝小虎马来发周晓根王柳静
Owner ZHEJIANG UNIV OF TECH
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