Protein structure prediction method based on tree structure replica exchange and fragment assembly

A protein structure and prediction method technology, applied in the field of three-dimensional structure prediction of protein structure, can solve problems such as inaccurate energy model, difficult protein folding problem, and huge protein conformation space

Active Publication Date: 2014-12-10
ZHEJIANG UNIV OF TECH
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Problems solved by technology

However, using computer computing power and optimization algorithms to predict the three-dimensional structure of proteins through protein sequence information, that is to say, the problem of protein folding is still a difficult problem.
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  • Protein structure prediction method based on tree structure replica exchange and fragment assembly
  • Protein structure prediction method based on tree structure replica exchange and fragment assembly
  • Protein structure prediction method based on tree structure replica exchange and fragment assembly

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Embodiment Construction

[0059] The present invention will be further described below in conjunction with the accompanying drawings.

[0060] refer to figure 1 and figure 2 , a method for protein structure prediction based on tree-structured copy exchange and fragment assembly

[0061] , the prediction method includes the following steps:

[0062] A1. For protein conformation processing, the ID number is 1ENH, and its sequence is RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKI. The process is as follows;

[0063] STEP1.1. According to the obtained protein amino acid sequence sequence, use the Rosetta package software pose_from_sequence function to construct a long protein chain;

[0064] STEP1.2, and use the Mover object SwitchResidueTypeSetMover built by Rosetta to obtain the long protein chain, and use its apply method to convert the all-atom conformation of the long protein chain into the bone chain atomic conformation. The protein conformation is represented by pose, which is always red...

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Abstract

The invention discloses a protein structure prediction method based on tree structure replica exchange and fragment assembly. The method includes the following steps that protein conformations are based on a replica exchange thought, on the basis that preservation of a plurality of replica messages is facilitated, protein conformation space search can be enhanced, the advantage of a tree data structure is used, energy layering and protein middle conformation shape information can also be used, a specific weight function is used for selecting the entire protein confirmation spaces through certain probability as compiled replicas, the protein conformations are led to step towards a low-energy path, the diversity of the protein conformations can be reserved to the greatest extent, and thus the purpose for predicting the protein native state can be achieved ultimately. By means of the protein structure prediction method based on tree structure replica exchange and fragment assembly, the calculated amount can be greatly reduced, computing time is shortened, and meanwhile it is guaranteed that the low-energy conformations can be searched for.

Description

technical field [0001] The invention relates to the field of computer application, bioinformatics, algorithm optimization, optimization theory, molecular informatics, and in particular to a method for predicting a three-dimensional structure of a protein structure. Background technique [0002] Bioinformatics reveals the biological mysteries of large and complex biological data through the comprehensive use of biology, computer science and information technology. It is a hot spot of current research. Bioinformatics research results have been widely used in sequence alignment, protein alignment, gene recognition analysis, molecular evolution, sequence contig assembly, genetic code, drug design, biological systems, protein structure prediction, etc. Among them, protein structure prediction is an important branch in the field of bioinformatics. [0003] Protein molecules play an important role in the cellular activities of organisms, and many activities of organisms are based...

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Application Information

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IPC IPC(8): G06F19/16
Inventor 张贵军秦传庆周晓根郝小虎梅珊陈先跑李章维
Owner ZHEJIANG UNIV OF TECH
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