Colony parallel computation accelerating method for calculating protein structure based on protein folding

Abstract

The invention discloses a colony parallel computation accelerating method which builds a constraint model for the protein folding process and conducts parallel acceleration on the iteration process ofcomputation on an isomeric colony computer. The method comprises the steps that approximate computation of protein folding computation is divided into a plurality of computation risks, each node is subjected to solution according to local computation risks and data back-up, and no data synchronization is conducted in the process; data synchronization is conducted after the node completes a plurality of time steps; the results of the computation risk of the node is compared with the local data back-up, if changes occur, the data is transmitted in the colony by broadcasting, the all the main hosts of the colony are informed to update the local back-up, so as to accordingly realize parallel computation acceleration for calculating the protein structure based on protein folding. The method can improve the computation speed and precision of calculating protein structure solution based on protein folding, reduce the communication cost in the computation process, and save the computation resources.

Description

technical field [0001] The invention belongs to the technical field of high-performance computing, and relates to a computing parallelization method, in particular to a method for parallelizing and accelerating the calculation of protein folding by using computer clusters. Background technique [0002] The problem of protein folding is to solve a sequence of amino acids to form a protein molecule with a specific three-dimensional structure through the interaction of amino acid residues. In practice, the dynamics simulation method can be used to establish the energy constraint equation during the protein folding process, and the three-dimensional structure of the protein can be predicted by means of numerical simulation based on the amino acid sequence. [0003] A linear equation system can be constructed for the energy constraints in the protein folding process, and the general form of the linear equation system is [0004] Ax=b [0005] Among them, A is a non-singular mat...

AI Technical Summary

Problems solved by technology

[0010] However, the above-mentioned existing methods are often based on a stand-alone form or are easily limited by communication, the degree of parallelization is not high, the acceleration effect is not ideal, and the solution scale is limited by the capacity of a stand-alone machine; An Effective Technical Solution for Parallel Acceleration

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