A Dynamic Step Size Search Method in Conformation Space

Abstract

The invention discloses a method of searching for the dynamic step length of a conformation space. The method comprises the following steps that the conformation space is layered according to energy and temperature, each layer of the conformation space is subdivided to obtain conformation rooms, and then initialization of the conformation space is completed; an amino acid sequence is disturbed randomly to obtain an initial conformation, energy values of the initial conformation are obtained by means of Rosetta Score3 calculation and are stored in the conformation rooms in corresponding energy layers, and then initialization of the conformation is completed; weights are distributed to the divided energy layers, different fragment assembly (FA) step lengths and Monte Carlo (MC) disturbance step lengths are given to the different energy layers, a temperature parameter list is set at the same time, and then initialization of system parameters is completed; the energy layers, the conformation rooms and the conformation are selected randomly and sequentially according to the weights, the conformation is expanded, whether the current conformation needs to be received is judged according to corresponding Metropolis criteria, and then updating of a conformation system is completed; the steps are carried out iteratively till the set number of iterations is reached. The method is an effective conformation space enhancement sampling method.

Description

technical field [0001] The invention relates to the fields of bioinformatics and computer applications, in particular to a method for searching dynamic steps in conformation space. 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. At present, protein structure prediction methods can be roughly divided into two categories, template-based methods and non-template-based methods. Among them, the non-template-based ab initio prediction (Ab-inito) method is the m...

AI Technical Summary

Problems solved by technology

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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