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Protein conformation space optimization method based on local structure comparison

A local structure and optimization method technology, applied in proteomics, used to analyze two-dimensional or three-dimensional molecular structure, genomics, etc., can solve the problems of low sampling efficiency and low prediction accuracy, so as to improve prediction accuracy and search efficiency effect

Active Publication Date: 2019-02-26
ZHEJIANG UNIV OF TECH
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Problems solved by technology

[0006] In order to overcome the shortcomings of low sampling efficiency and low prediction accuracy in the existing protein conformation space optimization methods, the present invention proposes a protein conformation space optimization method based on local structure alignment with high sampling efficiency and high prediction accuracy

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  • Protein conformation space optimization method based on local structure comparison
  • Protein conformation space optimization method based on local structure comparison
  • Protein conformation space optimization method based on local structure comparison

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Embodiment Construction

[0042] The present invention will be further described below in conjunction with the accompanying drawings.

[0043] refer to Figure 1 ~ Figure 3 , a method for optimizing protein conformation space based on local structure alignment, the method comprising the following steps:

[0044] 1) given input sequence information;

[0045]2) Select the Rosetta score3 energy function E(x), and obtain the fragment library according to ROBETTA;

[0046] 3) Parameter initialization: set the population size Ps, the iteration counter g, the maximum genetic algebra G max , initial population search track length N, fragment length m, parameter n;

[0047] 4) Initialize the population: start Ps Monte Carlo trajectories, search N times for each trajectory, and generate Ps initial individuals;

[0048] 5) For each target individual x i ,i∈{i=1,.2..,Ps} performs the following operations:

[0049] 5.1) Randomly select an individual x j ,j∈{1,2,...,Ps} and j≠i, perform crossover operation: ...

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Abstract

The invention provides a protein conformation space optimization method based on local structure comparison. Under the basic framework of an evolutionary algorithm, a search strategy based on local structure comparison is adopted, a segment insertion window is randomly selected, original segment information in conformation and segment information in a fragment library are compared through two independent structural indicators, a potential segment is selected for structural replacement according to the two structural comparison indicators, and finally, the population update is guided accordingto a Monte Carlo mechanism and a potential conformation is selected to enter a next generation of population. The protein conformation space optimization method based on local structure comparison provided by the invention has the advantages of high prediction precision and low computational cost.

Description

technical field [0001] The invention relates to the fields of biological informatics, intelligent optimization and computer application, and in particular to a protein conformation space optimization method based on local structure comparison. Background technique [0002] Proteins are the main bearers of life activities, and the diversity of their structures determines the diversity of their functions. Precisely predicting the spatial structure of proteins is of great significance to biopharmaceuticals and disease research. The use of biochemical methods to determine protein structures is costly and time-consuming. Therefore, the use of computational methods to predict the three-dimensional structure of proteins has gradually become an important topic in computational biology. [0003] In recent years, de novo prediction methods have achieved good results in the field of protein structure prediction. However, as far as the current technical means are concerned, the ab init...

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Application Information

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IPC IPC(8): G16B20/20G16B15/20
Inventor 张贵军王小奇谢腾宇周晓根马来发郝小虎
Owner ZHEJIANG UNIV OF TECH
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