Secondary structure spatial distance constraint-based protein conformation search method

A technology of secondary structure and spatial distance, applied in special data processing applications, instruments, electrical digital data processing, etc., can solve problems such as low sampling efficiency and low prediction accuracy, and achieve faster convergence speed, higher prediction accuracy, and more diversity. sexual effect

Active Publication Date: 2018-01-19
ZHEJIANG UNIV OF TECH
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Problems solved by technology

[0005] In order to overcome the shortcomings of low sampling efficiency and low prediction accuracy in existing protein structure prediction conformation space search methods, the

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  • Secondary structure spatial distance constraint-based protein conformation search method
  • Secondary structure spatial distance constraint-based protein conformation search method
  • Secondary structure spatial distance constraint-based protein conformation search method

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Embodiment Construction

[0030] The present invention will be further described below in conjunction with the accompanying drawings.

[0031] refer to Figure 1 ~ Figure 3 , a protein conformation search method based on secondary structure space distance constraints, said method comprising the following steps:

[0032] 1) given input sequence information;

[0033] 2) Parameter initialization: set the population size NP, the maximum genetic algebra G max , determine the crossover probability P c , the initial population iteration number iteration, the cross fragment length frag_length, the assembly counter reject_number, the maximum assembly number reject_max, the spatial length of the secondary structure in the prior knowledge and the feature vector formed by the spatial distance between the central residues of two adjacent secondary structures D = {d 1 ,...,d m , d 1,2 ,...,d k,k+1}, where d m is the length of the mth secondary structure block of the target protein, d k,k+1 is the spatial di...

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Abstract

The invention discloses a secondary structure spatial distance constraint-based protein conformation search method. According to the method, feature vectors are formed by utilizing a spatial length ofeach secondary structure in a target protein and information of spatial distance between central residues of every two adjacent secondary structures so as to serve as space limitation conditions under a basic framework of a genetic algorithm, so that a solution space is searched in a relatively small conformation space under the condition that an energy function is given; and meanwhile, the spatial distance information is added in a selection operator, so that the inaccuracy of the energy function is made up and then the accuracy of structure modeling is effectively improved. The invention discloses the secondary structure spatial distance constraint-based protein conformation search method which is relatively high in sampling efficiency, relatively high in prediction accuracy and low incalculation cost.

Description

technical field [0001] The invention relates to the fields of biological informatics, artificial intelligence optimization and computer application, and in particular to a protein conformation search method based on the spatial distance constraints of secondary structures. Background technique [0002] Protein is a biomacromolecule formed by the dehydration condensation of amino acids, which plays a decisive role in human health. Accurately grasping the structure and function of protein is of great significance to disease research and biopharmaceuticals. Currently, there are two main methods for protein structure prediction: experimental methods and theoretical predictions. Experimental methods include X-ray crystallography, nuclear magnetic resonance spectroscopy, and electron microscopy; although these methods can accurately determine the three-dimensional structure of some proteins, it is time-consuming and expensive to determine the structure through experimental methods...

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Application Information

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IPC IPC(8): G06F19/18
Inventor 张贵军王小奇马来发周晓根谢腾宇王柳静孙科
Owner ZHEJIANG UNIV OF TECH
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