Method for predicting protein structure based on phased multi-strategy copy exchange

A protein structure and prediction method technology, applied in the field of protein structure prediction based on phased multi-strategy copy exchange, can solve the problems of low sampling efficiency, low prediction accuracy and complexity, and high complexity

Active Publication Date: 2016-10-26
ZHEJIANG UNIV OF TECH
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Problems solved by technology

[0006] In order to overcome the shortcomings of low sampling efficiency, high complexity and low prediction accuracy in existing protein structure prediction, the

Method used

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  • Method for predicting protein structure based on phased multi-strategy copy exchange
  • Method for predicting protein structure based on phased multi-strategy copy exchange
  • Method for predicting protein structure based on phased multi-strategy copy exchange

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Embodiment Construction

[0039] The present invention will be further described below in conjunction with the accompanying drawings.

[0040] refer to Figure 1 ~ Figure 2 , a protein structure prediction method based on staged multi-strategy replica exchange, including the following steps:

[0041] 1) given query sequence information;

[0042] 2) Initialization: Set the population size NP, variation factor F, crossover probability CR, n temperature layers T, iteration number iteration, segment length L, energy function Rosetta Score3, firstly through random folding and transformation of the query sequence, in Each temperature layer generates an initial conformational population of size NP, the initial population is P={x i |i∈I}, calculate the energy value f(x i ), i∈I, and let Where i is the individual number of the population, I is the set of individual numbers of the population, I={1,2,...,NP}, is the minimum value in the energy function value corresponding to the temperature layer, and T is...

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Abstract

This invention discloses a method for predicting protein structure based on phased multi-strategy copy exchange. In the frame of differential evolution (DE), generate initial conformation populations with a variety of folding types in each temperature layer; to each temperature layer, divide a conformation search into two phases according to iterations; randomly select a conformation as a target unity from the populations in the first phase; divide the populations into two parts according to energy in the second phase; randomly select one unity as the target unity from first 50% of populations with low energy; randomly select three conformation unities different from the target unity to generate a testing unity through variation, cross and section combination strategy; judge whether to accept the testing unity according to the energy of the conformation so as to perform copy exchange to corresponding unities of adjacent temperature layers; and, under the guidance of the phased strategy and the supplement of copy exchange strategy, acquire a series of metastable conformation through updating continuously.

Description

technical field [0001] The invention relates to the fields of bioinformatics and computer applications, and in particular to a protein structure prediction method based on staged multi-strategy copy exchange. Background technique [0002] Developing a computer algorithm that can predict a protein's structure from its amino acid sequence is a huge challenge. On the one hand, knowledge of the native structure is a starting point for understanding biological mechanisms and for discovering drugs that inhibit or activate proteins. On the other hand, we know more about structures than sequences, and this gap is widening due to the development of high-throughput sequencing technologies. Therefore, methods that can accurately predict the structure of a sequence are of considerable value. [0003] In the CASP (Assessment of Protein Structure Prediction) competition, which began in 1994, Moult and his colleagues accelerated the process of computer-based protein structure prediction....

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Application Information

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IPC IPC(8): G06F19/16
CPCG16B15/00
Inventor 张贵军俞旭锋周晓根郝小虎王柳静
Owner ZHEJIANG UNIV OF TECH
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