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A Multimodal Protein Structure Prediction Method Based on Niche Resampling

A protein structure and prediction method technology, applied in the field of multimodal protein structure prediction based on niche resampling, can solve the problems of insufficient sampling ability, low sampling efficiency, inaccurate energy function, etc., to improve the overall prediction accuracy, increase The effect of conformational diversity

Active Publication Date: 2021-08-03
ZHEJIANG UNIV OF TECH
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Problems solved by technology

[0006] In order to overcome the problems of inaccurate energy function, insufficient sampling capacity, low sampling efficiency, and insufficient prediction accuracy of existing protein structure prediction methods, the present invention provides a multimodal protein structure prediction method based on niche resampling

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  • A Multimodal Protein Structure Prediction Method Based on Niche Resampling

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Embodiment Construction

[0035] The present invention will be further described below in conjunction with the accompanying drawings.

[0036] refer to Figure 1 to Figure 3 , a multimodal protein structure prediction method based on niche resampling, the method comprising the following steps:

[0037] 1) Input the sequence information of the target protein;

[0038] 2) Obtain the fragment library files of 3 fragments and 9 fragments from the ROBETTA server (http: / / www.robetta.org / ) according to the target protein sequence;

[0039] 3) Setting parameters: maximum number of iterations G, energy function coefficient k 1 , niche radius coefficient k 2 , degradation function coefficient m, energy threshold T;

[0040] 4) Set g=1, g∈{1,2,...,G};

[0041] 5) Energy function initialization: record P as the target conformation, and set Rosetta's initial energy function as M 1 (P) = score(P);

[0042] 6) Conformation initialization: Random fragment assembly produces an initial conformation

[0043] 7)...

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Abstract

A multimodal protein structure prediction method based on niche resampling, in the Monte Carlo framework, firstly, the initial energy function is used for the first round of search; secondly, the lowest energy conformation obtained after each run is used as the initial Conformation, resampling in the current niche; thirdly, calculate the radius of the niche according to the conformation information obtained by resampling, and construct an energy function for the next round of search, so as to avoid the searched conformation repeatedly falling into the local optimum; finally , and output the conformation with the lowest energy in each resampling process as the final prediction result. The multimodal protein structure prediction method based on niche resampling can alleviate the problem that the sequence niche method is difficult to determine the radius, so as to enhance the sampling ability, improve the sampling efficiency and improve the prediction accuracy. The invention provides a multimodal protein structure prediction method based on niche resampling with high prediction accuracy.

Description

technical field [0001] The invention relates to the fields of bioinformatics and computer applications, and in particular to a multimodal protein structure prediction method based on niche resampling. Background technique [0002] Protein is the building block of life, and its structure determines its special biological function. Obtaining accurate protein folding structures is crucial for understanding protein folding mechanisms, analyzing protein functions, and developing innovative drugs. "Science" magazine also listed protein structure prediction as one of the 125 cutting-edge scientific issues in the 21st century. Therefore, how to accurately obtain the three-dimensional structure of proteins and clarify their relationship with biological functions is a serious challenge. [0003] Biological wet experiment is a traditional method to determine the three-dimensional structure of protein, such as X-ray diffraction, nuclear magnetic resonance, cryo-electron microscopy, et...

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): G16B15/20G16B30/00
CPCG16B15/20G16B30/00
Inventor 张贵军夏瑜豪赵凯龙刘俊彭春祥周晓根
Owner ZHEJIANG UNIV OF TECH
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