Protein structure prediction method based on multi-population ensemble mutation strategies
A protein structure and prediction method technology, applied in the field of protein structure prediction, can solve the problems of low sampling efficiency, low prediction accuracy, poor population diversity, etc.
Active Publication Date: 2019-03-22
ZHEJIANG UNIV OF TECH
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[0007] In order to overcome the shortcomings of the existing protein structure prediction methods, such as low sampling efficiency, poor population diversity, and low prediction accuracy, the present invention introduces a multi-population mutation strategy to guide conformational space optimization under the framework of the basic differential evolution algorithm, and proposes a sampling efficiency Protein structure prediction method based on multigroup ensemble mutation strategy with high prediction accuracy
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[0043] The present invention will be further described below in conjunction with the accompanying drawings.
[0044] refer to Figure 1 ~ Figure 3 , a protein structure prediction method based on multiple group ensemble variation strategies, the prediction method comprising the following steps:
[0045] 1) The sequence information of the given target protein;
[0046] 2) Obtain fragment library files from the ROBETTA server (http: / / www.robetta.org / ) according to the target protein sequence, including 3-fragment library files and 9-fragment library files;
[0047] 3) Obtain the distance spectrum file from the QUARK server (https: / / zhanglab.ccmb.med.umich.edu / QUARK / ) according to the sequence information;
[0048] 4) Setting parameters: population size NP, maximum iteration algebra G of the algorithm, crossover factor CR, temperature factor β, set iteration algebra g=0;
[0049] 5) Population initialization: Random fragment assembly generates NP initial conformations C i , i...
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Provided is a protein structure prediction method based on multi-population ensemble mutation strategies. Under the framework of an evolutionary algorithm, firstly, a population is divided into four subpopulations on average, and different mutation strategies are designed respectively for each subpopulation; secondly, according to a Rosetta energy function score3, a range error coefficient and a Monte Carlo probability acceptance criteria, conformational selection is executed to guide the renewal process of conformation, the problem can not only alleviated that an energy function is not accurate, algorithm sampling can also be guided to obtain a conformation with lower energy and a more reasonable structure, and meanwhile the sampling efficiency is improved. The protein structure prediction method based on multi-population ensemble mutation strategies has high sampling efficiency and prediction accuracy.
Description
technical field [0001] The invention relates to the field of bioinformatics and computer application, in particular to a method for predicting protein structure based on multigroup ensemble variation strategy. Background technique [0002] The rapid development of computer hardware and software technology provides a solid basic platform for the development of ab initio prediction methods. The progress and breakthroughs in protein structure prediction methods have further promoted the extensive participation of researchers in computer science and evolutionary computing, making it the most active multidisciplinary research topic in the field of protein structure prediction in recent years. In a review article published in the journal Science in 2012, Professor Dill, an academician of the American Academy of Sciences, reviewed the progress made in the field of de novo prediction in the past 50 years, and pointed out that in the process of seeking answers to this question, super...
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IPC IPC(8): G16B30/10
Inventor 张贵军彭春祥周晓根刘俊王柳静胡俊
Owner ZHEJIANG UNIV OF TECH