Protein structure ab initio prediction method based on bacterial oraging optimization algorithm

A technology of protein structure and prediction method, which is applied in the field of ab initio prediction of protein structure based on bacterial population optimization algorithm, can solve the problems of weak conformational space sampling ability and insufficient conformation update accuracy, and achieve the effect of reducing calculation cost and improving sampling ability

Inactive Publication Date: 2017-10-03
ZHEJIANG UNIV OF TECH
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[0005] At present, the main technical bottleneck lies in two aspects. The first aspect lies in th

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  • Protein structure ab initio prediction method based on bacterial oraging optimization algorithm
  • Protein structure ab initio prediction method based on bacterial oraging optimization algorithm

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

[0037] Reference figure 1 , A protein structure ab initio prediction method based on flora optimization algorithm, including the following steps:

[0038] 1) Select Rosetta Score3 as the protein force field model, that is, the energy function J(C), C represents the protein conformation;

[0039] 2) Given the input sequence information, obtain the target protein fragment library through the free web server Robetta Server;

[0040] 3) Parameter initialization: the population size of the bacteria NP, NP is an even number, the step size of the i-th bacterium for chemotaxis behavior i ,i∈{1,...,NP}, the number of cycles of bacterial chemotaxis behavior N c , The maximum number of advances in the chemotaxis cycle N s , The number of bacterial reproduction behaviors N re , The number of times the bacteria perform migration behavior N ed , The migration probability P ed ;

[0041] 4) Use dihedral a...

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Abstract

The invention provides a protein structure ab initio prediction method based on a oraging optimization algorithm. The method comprises the steps of making a conformation dihedral angle advance in the random direction according to the property that a bacteria swarm has chemotaxis and aggregation and a natural law of survival of the fittest of the bacteria swarm, and accepting low-energy conformations; eliminating half high-energy conformations after the conformation are aggregated, and using the low-energy conformations to conduct propagation and generate the filial generation; in addition, adopting a migration mechanism to conduct segment assembly on an individual to avoid the situation that the individual falls into local minimum and premature convergence as much as possible, so that the diversity of a group is guaranteed, and therefore the conformation space sampling capacity is effectively improved. The protein structure ab initio prediction method based on the oraging optimization algorithm not only is high in prediction precision, but also is small in calculation cost.

Description

technical field [0001] The present invention relates to a field of biological informatics, intelligent optimization, and computer application, and in particular to a method for ab initio prediction of protein structure based on a flora optimization algorithm. Background technique [0002] Protein is one of the most important macromolecules in all living things, and more than half of the dry weight of a cell is protein. Proteins are sequential chains of amino acids linked together by single peptide bonds, and these linked chains fold into three-dimensional structures that embody their functions and regulate cellular activities in organisms to maintain life. Protein molecules embody the remarkable relationship between protein structure and function at the molecular level. Proteins have many different functions in biology. The three-dimensional natural structure of a protein determines its biological mechanism, and in turn, the one-dimensional chain of protein amino acid mono...

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Application Information

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IPC IPC(8): G06F19/18G06N3/00
CPCG06N3/006G16B20/00
Inventor 张贵军谢腾宇郝小虎周晓根王柳静
Owner ZHEJIANG UNIV OF TECH
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