Geodesic
Optimization of modeling immobilized protein interactions on compulational clusters with the supplying of access to the algorithm via web-interface
Vestnik Ûžno-Uralʹskogo gosudarstvennogo universiteta. Seriâ Vyčislitelʹnaâ matematika i informatika, Tome 3 (2014) no. 1, pp. 55-67
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In this work were introduced parallel versions based on OpenMP and MPI technologies of sequential program for modeling immobilized protein interactions. Both versions have shown goodscalability and better time indices to compare with the sequential version when running on singleprocessor. Need to mention that modeling of immobilized protein interactions for some compoundshave taken more than twenty hours of computations on several hundreds of processors, that's why for such modeling tasks with the great quantity of positions availability of nondeterministicalgorithms, providing biologically correct result in reasonable time, seems to be rather important. Selection of stochastic algorithms has proved its value: both Monte-Carlo and simulated bee colonyalgorithms had found conformation corresponding minimal energy state. Supplying of access to thealgorithm via web-interface measures up modern specifications of remote computations and allowsthe wide circle of specialists use computational power of Moscow State University and, taking intoaccount extending the sphere of application tasks of molecular simulation, the presence of openweb-interface providing remote access to the computational clusters is quite an important task.
Keywords: bioinformatics, multiprocessor systems, immobilized protein interactions, parallel algorithms, stochastic algorithms. 
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K. V. Romanenkov; A. N. Salnikov. Optimization of modeling immobilized protein interactions on compulational clusters with the supplying of access to the algorithm via web-interface. Vestnik Ûžno-Uralʹskogo gosudarstvennogo universiteta. Seriâ Vyčislitelʹnaâ matematika i informatika, Tome 3 (2014) no. 1, pp. 55-67. http://geodesic.mathdoc.fr/item/VYURV_2014_3_1_a4/

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