Abstract
We have developed an object oriented large-scale scientific simulations system that contains algorithms of molecular scientific computing programs, called Embedded High-Performance Computing (EHPC). As an application of the system, "EHPC-Drug platform" has been constructed for rational drug design. It can provide a high-performance computing ability for exhaustive conformational analyses of biomolecules, generating computation of their three-dimensional topological descriptors, and docking calculations with their target receptors. To enhance its computing abilities, we are also planning to apply Grid computing technology to this system for parallel and distributed computing and Grid Data processing. As a critical test of our approach, we applied it to a prediction of bound conformation of several HIV protease inhibitors with the protease.
