Protein Structure Prediction Based On Grid Parallel Implementation

Protein structure prediction (PSP) is a hot research topic in current biology. By limits of itsspecial structure and its model, using non-deterministic polynomial (NP) problem to getminimum energy value, which infer to folding structure, is one of the research direction withthis problem. There are many algorithms with this problem, but all of them have long timeconsumption because of the complexity of the calculations. Genetic annealing algorithm (GAA)combining with simulated annealing algorithm and genetic algorithm, which combining withthe advantages of global searching ability of genetic algorithm and local convergence ofannealing algorithm, is a common algorithm for PSP.Grid computing is a kind of distributed parallel computing, it is committed to us ing theidle resources on the network to solve large-scale computing problems. The design of gridsystem based on the grid middleware, which have characteristics of strong management,highsafety, convenient transfer of data and good scalability, is suitable for large-scale computationalproblems in general studies consider to a computational efficiency, equipment cost. Gridprogramming interface based on MPI is an application of the grid computing.This paper aims to solve the problem of PSP with GAA, transplant the serial algorithm toparallel grid platform. In the parallel algorithm, the population is divided into many sub-populations and these sub-populations are distributed to child nodes to do evolutionaryoperation respectively. At the same time we improve the algorithm operator (selection,crossover, mutation) according to the actual situation in order to achieve better computationalspeed and the efficiency of the algorithm.