A Grid Platform Construction For Drug Design

With the rapid development of X-ray crystallographic and nuclear magnetic resonance (NMR) techniques, more and more three dimensions (3-D) protein structures are known by people, which makes a promising future for DMD (drug-molecular discovery). However, DMD suffers the problems that, firstly, the searching space of drug molecular docking is huge, which includes 10~30 solutions at least even if only flexibility of ligand is considered, Furthermore, if billions of compounds are to be screened in this way, the computational power that is required becomes a limiting feature.The technology of grid has made a great deal of progress in the recent years. Grid can give the users general computational ability and resources, which are irrelative to any given location or equipments. Grid is representation of advanced technology and infrastructure, and it is a great progress after Internet. Combining virtual screening with grid computing will be valuable in drug design. Drug Discovery Grid (DDG) is developed based on this background. The time for docking of some ligands and a molecule can be reduced greatly by using DDG.The main contributions of this paper are summarized as follows. (1) Construct a grid platform of research and testing for new drug discovery;(2) Construct a node of DDG on DeepComp 1800 in Dalian University of Technology;(3) Improve the virtual screening algorithm of DDG, and develop a program for grid computing;(4) Give Make a time contrast between the way of DDG and this parallel program.The research work is supported by the Special Funds for Major State Basic Research Project (No.2004CB518901) of China.