Spatial optimization method for population protein conformation based on diversity indicators

An optimization method and diversity technology, applied in the fields of bioinformatics and computer applications, can solve problems such as low sampling efficiency, poor conformational diversity, and high complexity

Active Publication Date: 2018-09-28
ZHEJIANG UNIV OF TECH
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Problems solved by technology

[0005] In order to overcome the shortcomings of the existing protein structure prediction methods, such as low sampling efficiency, poor conformational diversity, high complexity, and low prediction accuracy, the present invention measures conformationa...

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  • Spatial optimization method for population protein conformation based on diversity indicators
  • Spatial optimization method for population protein conformation based on diversity indicators
  • Spatial optimization method for population protein conformation based on diversity indicators

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Embodiment Construction

[0046] The present invention will be further described below in conjunction with the accompanying drawings.

[0047] refer to figure 1 and figure 2 , a population protein conformation space optimization method based on a diversity index, said optimization method comprising the following steps:

[0048] 1) given input sequence information;

[0049] 2) Setting parameters: population size NP, recombination factor RC, maximum iteration number G max , diversity acceptance probability p;

[0050] 3) Use PSIPRED to predict the secondary structure information of the query sequence;

[0051] 4) Initialization: Firstly, generate an initial population P={x i |i∈I}, where i is the number of individuals in the population, I is the set of numbers of individuals in the population, I={1,2,...,NP}, x i Represents the i-th individual;

[0052] 5) Use the local search strategy of the second stage of Rosetta to assemble the fragments of each population individual to form a new population;...

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Abstract

A spatial optimization method for population protein conformation based on diversity indicators, comprising the steps of: firstly using the first stage of Rosetta to assemble in segments to generate an initial population, and using the second stage of Rosetta to assemble in segments to generate a new population; then performing Loop exchange on the conformation for the randomly selected Loop region to realize population reorganization; secondly, mutating each conformation based on the Loop region, merging all new individuals generated by the mutation with the current population, extracting theUSR characteristic information of the conformation to establish a diversity index, and updating the entire population based on the index and energy; finally, further optimizing the entire populationrespectively using the third and fourth stages of Rosetta to obtain the final prediction result. The invention has high sampling efficiency, good diversity, low complexity and high prediction precision.

Description

technical field [0001] The invention relates to the fields of bioinformatics and computer applications, in particular to a method for optimizing population protein conformation space based on diversity indexes. Background technique [0002] Bioinformatics is a research hotspot in the intersection of life science and computer science. Bioinformatics research results have been widely used in gene discovery and prediction, gene data storage and management, data retrieval and mining, gene expression data analysis, protein structure prediction, gene and protein homology relationship prediction, sequence analysis and comparison, etc. . The genome specifies all the proteins that make up the organism, and the genes specify the sequence of amino acids that make up the proteins. Proteins determine the function of cells, linking cell activities to life. The three-dimensional structure of a protein is one of the main determinants of its unique functional properties. Determination of...

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Application Information

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IPC IPC(8): G06F19/16
CPCG16B15/00
Inventor 张贵军彭春祥刘俊周晓根王柳静
Owner ZHEJIANG UNIV OF TECH
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