OPTIMIZATION OF MODELING IMMOBILIZED PROTEIN INTERACTIONS ON COMPULATIONAL CLUSTERS WITH THE SUPPLYING OF ACCESS TO THE ALGORITHM VIA WEB-INTERFACE

Abstract

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 good scalability and better time indices to compare with the sequential version when running on single processor. Need to mention that modeling of immobilized protein interactions for some compounds have taken more than twenty hours of computations on several hundreds of processors, that is why for such modeling tasks with the great quantity of positions availability of nondeterministic algorithms, 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 colony algorithms had found conformation corresponding minimal energy state. Supplying of access to the algorithm via web-interface measures up modern specifications of remote computations and allows the wide circle of specialists use computational power of Moscow State University and, taking into account extending the sphere of application tasks of molecular simulation, the presence of open web-interface providing remote access to the computational clusters is quite an important task.