Multi-objective optimization protein structure prediction method based on residue contact diagram

A protein structure and multi-objective optimization technology, applied in the field of multi-objective optimization protein structure prediction based on residue contact graph, can solve the problem of insufficient prediction accuracy of protein structure, achieve the effect of increasing population diversity and improving prediction accuracy

Pending Publication Date: 2020-12-15
ZHEJIANG UNIV OF TECH
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Problems solved by technology

[0005] In order to alleviate the problem of insufficient accuracy of protein structure prediction caused by inaccurate contact information of a single residue pair, the present invention provides a multi-objective optimized protein structure prediction method based on the residue contact map. Under the fram

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  • Multi-objective optimization protein structure prediction method based on residue contact diagram
  • Multi-objective optimization protein structure prediction method based on residue contact diagram
  • Multi-objective optimization protein structure prediction method based on residue contact diagram

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[0036] The present invention will be further described below in conjunction with the accompanying drawings.

[0037] refer to figure 1 and figure 2 , a multi-objective optimal protein structure prediction method based on residue contact map, the method comprises the following steps:

[0038]1) Input the sequence information of the target protein, use TripletRes server (zhanglab.ccmb.med.umich.edu / ResTriplet), MetaPSICOV server (bioinf.cs.ucl.ac.uk / psipred), RaptorX server (raptorx.uchicago.edu) / ContactMap), STOP-Contact server (sparks-lab.org / server / spot-contact) to predict the residue contact map of the target sequence;

[0039] 2) Obtain fragment library files of 3 fragments and 9 fragments from ROBETTA server (http: / / www.robetta.org / ) according to the target protein sequence;

[0040] 3) According to the confidence between residue pairs in the residue contact map, arrange the confidence of residue pairs in descending order, and select the first 2L contact information, ...

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Abstract

The invention discloses a multi-objective optimization protein structure prediction method based on a residue contact diagram. The method comprises the following steps: firstly, predicting the residuecontact diagram of a target protein sequence by utilizing Triplet Res, MetaPSICOV, RaptorX and STOPConact; secondly, designing a scoring function to initialize the population; then, sampling the population through fragment recombination and assembly; and finally, for different prediction servers, calculating according to a designed conact energy function to obtain four conact energies, sorting all conformations in the population through a weighted scoring function Etotal (Cn) which harmonizes an average number and a standard deviation, and selecting a first conformation in the last generationas a prediction result. According to the invention, protein misfolding caused by inaccurate prediction of a single residue contact pattern can be relieved, so that the diversity is increased, and theoverall prediction precision is improved.

Description

technical field [0001] The invention relates to the fields of bioinformatics and computer applications, in particular to a multi-objective optimization protein structure prediction method based on a residue contact map. Background technique [0002] Protein is the cornerstone of life, almost all cellular activities involve protein, and the three-dimensional structure of protein determines its special biological function. Therefore, protein structure information is crucial in protein research. For example, the catalytic function of an enzyme is performed by a part of the protein chain, that is, the active site exposed on the surface of the protein. Interactions between proteins and between proteins and molecules of nucleic acids, inhibitors, and activators are also limited to specific protein surface areas. Therefore, it is only possible to design targeted drugs that interact with protein surfaces if the protein structure is known. At present, the protein structure is main...

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Application Information

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IPC IPC(8): G06Q10/04G16B15/00G16B30/10G06N3/00
CPCG06N3/006G06Q10/04G16B15/00G16B30/10
Inventor 张贵军陈芳彭春祥李亭刘俊周晓根
Owner ZHEJIANG UNIV OF TECH
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