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Residue contact information auxiliary evaluation-based protein structure prediction method

A protein structure and prediction method technology, which is applied in the field of protein structure prediction based on residue contact information assisted evaluation, can solve the problems of insufficient precision to accurately search for near-natural state regions, and reduce prediction accuracy, so as to improve prediction accuracy and improve The effect of search efficiency

Active Publication Date: 2019-01-15
ZHEJIANG UNIV OF TECH
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Problems solved by technology

However, the accuracy of the current force field model is not enough to accurately search for the near-natural state region, resulting in lower prediction accuracy
[0005] Therefore, the existing energy function-based protein structure prediction methods have shortcomings in terms of efficient conformational space search and prediction accuracy, and need to be improved

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  • Residue contact information auxiliary evaluation-based protein structure prediction method
  • Residue contact information auxiliary evaluation-based protein structure prediction method
  • Residue contact information auxiliary evaluation-based protein structure prediction method

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Embodiment Construction

[0041] The present invention will be further described below in conjunction with the accompanying drawings.

[0042] refer to figure 1 and figure 2 , a protein structure prediction method based on residue contact information assisted evaluation, comprising the following steps:

[0043] 1) Given the input sequence information, use the Robetta server (http: / / robetta.bakerlab.org / ) to obtain the fragment library of the sequence;

[0044] 2) Use RaptorX-Contact (http: / / raptorx.uchicago.edu / ContactMap / ) to predict the contact map of the sequence, and obtain N residue pairs with a contact probability greater than 0.6. Contact means that the Cα-Cα Euclidean distance is less than The exposure probability is denoted as P k , k∈{1,...,N};

[0045] 3) Initialization: population size NP, the maximum number of iterations of the first and second stages of the population are G1 and G2 respectively, according to the input sequence, execute the first and second stages of the Rosetta Abinit...

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Abstract

The invention relates to a residue contact information auxiliary evaluation-based protein structure prediction method. According to the method, a fragment library and a contact map are obtained through Robetta and RaptorX-Contact; the contact map is used to auxiliarily evaluate conformations with different ways in two stages of population evolution; and a final prediction result is obtained through clustering. According to the method of the invention, contact map information is adopted to auxiliarily evaluate conformations, and conformations with correct topology are reserved; and therefore, search efficiency and prediction accuracy can be improved. The residue contact information auxiliary evaluation-based protein structure prediction method of the invention has high prediction precision.

Description

technical field [0001] The invention relates to the fields of biological informatics, intelligent optimization and computer application, and in particular to a protein structure prediction method based on residue contact information assisted evaluation. Background technique [0002] Protein structure refers to the spatial structure of protein molecules. Protein is mainly composed of carbon, hydrogen, oxygen, nitrogen and other chemical elements. It is an important class of biological macromolecules. All proteins are polymers formed by connecting 20 different amino acids. After forming proteins, these amino acids are also called for the residue. Protein sizes can range from this lower limit all the way up to thousands of residues. The currently estimated average length of proteins varies in different species, generally about 200-380 residues, and the average length of proteins in eukaryotes is about 55% longer than that in prokaryotes. Larger protein aggregates can be form...

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Application Information

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IPC IPC(8): G16B15/30
Inventor 张贵军谢腾宇孙科周晓根郝小虎王柳静
Owner ZHEJIANG UNIV OF TECH
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