Protein structure predicating method based on tree search and fragment assembly

Abstract

The invention relates to a protein structure predicating method based on tree search and fragment assembly. The protein structure predicating method comprises the following steps that A1, a pdb format file of protein is obtained, and in addition, required data is cleaned out; A2, a fragment library is generated; A3, a force field model is selected; A4, a score 3 energy function of Rosetta is adopted; A5, the whole energy landscape is subjected to discretization, in addition, each layer is further subjected to discretization and is divided into individual block regions, an energy layer is randomly selected according to the energy weight in each search, in addition, one block region is selected according to the probability at the energy layer, if conformation is contained in the block region, a fragment assembly method is adopted, one fragment on a sequence is randomly selected, then, one fragment is randomly selected in the fragment library, a target fragment on the sequence is replaced, the Monte Carlo criterion is used for judging whether the conformation is accepted or not, and if the conformation is accepted, the conformation is put into a set. The protein structure predicating method has the advantages that the calculation quantity and the calculation time can be greatly reduced, and the condition that conformation with lower energy can be searched is ensured.

Description

technical field [0001] The present invention relates to the fields of computer application, bioinformatics, optimization theory, molecular biology, etc., and particularly relates to a method for predicting the three-dimensional structure of proteins, which belongs to the application of modern intelligent optimization methods to the prediction of three-dimensional protein structures. 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. Anfinsen, the...

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Problems solved by technology

[0007] However, it is very unscientific to use exhaustive search to traverse the entire energy landscape. First of all, if you want to traverse the entire energy landscape, the amount of calculation is very large. This value is related to the smallest unit value after discretizing the energy landscape. , the finer the discretization, the greater the amount of calculation, the higher the corresponding time cost, and the more computer resources required

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