A method for searching population conformation space based on replica exchange and local enhancement strategy
A spatial search and local enhancement technology, applied in the field of computer applications and bioinformatics, can solve the problems of insufficient conformation update accuracy and weak conformational spatial sampling ability, achieve diversity and enhanced spatial sampling ability, improve convergence speed, improve The effect of prediction accuracy
Active Publication Date: 2018-06-01
ZHEJIANG UNIV OF TECH
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But so far there is no perfect method to predict the three-dimensional structure of proteins. Even if good prediction results are obtained, it is only for some proteins. At present, the main technical bottlenecks lie in two aspects. First, On the one hand, it lies in the sampling method. The existing technology is not strong in sampling the conformation space;
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[0040] The present invention will be further described below in conjunction with the accompanying drawings.
[0041] refer to figure 1 , a population conformation space search method based on replica exchange and local enhancement strategies, including the following steps:
[0042] 1) given input sequence information;
[0043] 2) Set system parameters: population size popSize, algorithm iteration number T, crossover factor CR, segment length L, replica layer number RE, replica layer temperature parameter kT;
[0044]3) Population initialization: at each replica layer, popSize population individuals P are generated from the input sequence init ;
[0045] 4) Start iteration, execute the population update process in each copy layer, for each individual in the initial population:
[0046] 4.1) Let i=1, where i∈{1,2,3,...,popSize}; let P target =P i , where i is the serial number, P target represent the target individual;
[0047] 4.2) Randomly generate positive integers ra...
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A replica exchange and local enhancement strategy-based group conformation space search method is provided by the invention. Under a frame of a differential evolution algorithm, a Rosetta Score 3 coarse-grained knowledge energy model is used to effectively lower the number of conformation space search dimensions and improve a convergence rate of an algorithm; introducing a knowledge-based fragment assemble technique can effectively improve prediction precision; by using good local search performance of a Monte Carlo algorithm, local enhancement is performed on a population so as to obtain more excellent local conformation; combining a strong global search ability of the differential evolutionary algorithm can perform more effective sampling on a conformation space; and introducing a replica exchange strategy can further enhance diversity of the population and ability of spatial sampling.
Description
technical field [0001] The invention relates to the fields of bioinformatics and computer applications, and in particular to a search method for group conformation space based on copy exchange and local enhancement strategies. Background technique [0002] Protein molecules play a vital role in the process of biological and cellular chemical reactions. Their structural models and bioactive states have important implications for our understanding and cure of many diseases. Only when proteins are folded into a specific three-dimensional structure can they produce their unique biological functions. Therefore, to understand the function of a protein, it is necessary to obtain its three-dimensional structure. [0003] Protein tertiary structure prediction is an important task in bioinformatics. The biggest challenge facing the protein conformation optimization problem is to search the extremely complex protein energy function surface. The protein energy model takes into accou...
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IPC IPC(8): G06F19/16
Inventor 张贵军郝小虎俞旭锋周晓根陈凯徐东伟
Owner ZHEJIANG UNIV OF TECH