Sub-population co-evolution-based protein structure prediction method

A protein structure and prediction method technology, which is applied in the field of protein structure prediction based on subpopulation co-evolution, can solve the problems of low prediction accuracy and search efficiency, and achieve the effects of increasing diversity, improving search efficiency, and improving prediction accuracy

Active Publication Date: 2019-01-22
ZHEJIANG UNIV OF TECH
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Problems solved by technology

[0006] In order to overcome the shortcomings of low prediction accuracy and search efficiency of existing protein conformation space optimization methods, the present invention proposes a protein structure prediction method based on co-evolution of subpopulations with high prediction accuracy and search efficiency

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  • Sub-population co-evolution-based protein structure prediction method
  • Sub-population co-evolution-based protein structure prediction method
  • Sub-population co-evolution-based protein structure prediction method

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Embodiment Construction

[0038] The present invention will be further described below in conjunction with the accompanying drawings.

[0039] refer to Figure 1 ~ Figure 3 , a protein structure prediction method based on co-evolution of subpopulations, including the following steps:

[0040] 1) Input the sequence information of the protein to be tested, and obtain the fragment library from the ROBETTA server (http: / / www.robetta.org / );

[0041] 2) Parameter setting: set the population size NP, the number of subpopulations N, the crossover probability CR, the fragment length l, the temperature factor KT, and the maximum number of iterations G max , and initialize the number of iterations g=0;

[0042] 3) Randomly select fragments from the fragment library corresponding to each residue to assemble and generate an initial conformation population P={C 1 ,C 2 ,...,C NP}, and randomly divide the entire population into N equal-sized subpopulations, where N≥4, C i ,i={1,2,…,NP} is the i-th conformational...

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Abstract

The invention relates to a sub-population co-evolution-based protein structure prediction method. According to the method, a whole population is divided into a plurality of sub-populations of the samescale; as for the first sub-population, conformations are selected from the other different sub-populations so as to be subjected to variation; as for the second subpopulation, an optimal conformation in a subpopulation where a target conformation is located and conformations in the other subpopulations are selected so as to be subjected to variation; as for the third subpopulation, an optimal conformation in the entire population and the conformations in the other subpopulations are selected so as to be subjected to variation; and as for the other subpopulations, conformations are selected from the subpopulation where the target conformation is located and the other subpopulations are selected so as to be subjected to variation; and a test conformation is updated according to the Boltzmann probability. The sub-population co-evolution-based protein structure prediction method provided by the invention has the advantages of high prediction accuracy and high search efficiency.

Description

technical field [0001] The present invention relates to the fields of biological informatics, intelligent optimization and computer application, in particular to a method for predicting protein structure based on co-evolution of subpopulations. Background technique [0002] Biological cells contain many folded proteins formed by long chains of more than 20 amino acids. DNA is translated into an amino acid sequence of a protein with a codon of three nucleotides. Compared with the first genetic code, the corresponding relationship between the primary structure of the protein sequence and its tertiary structure (that is, the second genetic code or fold cipher) remains an unsolved mystery. However, misfolding of protein tertiary structure can lead to protein folding diseases such as diabetes, cataract, and Alzheimer's disease. Therefore, knowing the three-dimensional structure of the corresponding protein is a prerequisite for the realization of the treatment of these protein ...

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G16B15/00G16B20/00G16B40/00G06N3/00G06N3/12
CPCG06N3/006G06N3/126
Inventor 周晓根张贵军彭春祥胡俊刘俊
Owner ZHEJIANG UNIV OF TECH
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