Research On The Key Issues Of Docking Application In Heterogeneous Grid Environment

Molecular docking is a significant approach of drug discovery. It aims to find the candidate lead compounds from the millions of small molecular compounds with a specific target protein by using in silico (computer) analysis. Molecular docking is a compute-intensive task that requires a lot of computing resources. Currently, more and more chemists turn to powerful Grid platforms to carry out molecular docking to reduce the cost of drug discovery. However, existing Grid platforms usually have different standards and access interfaces, causing Grid resource islands that make chemists cannot use Grid resources effectively. Therefore, how to improve the utilization of heterogeneous Grid resources is a new challenge.In this paper we put efforts into the key issues of performing docking application in heterogeneous Grid environment by using one of the popular docking software——Dock. We achieve the resource utilization of two heterogeneous Girds—CGSP and GOS,which are supported by Education Department and NSFC respectively. The approach hides the complexity of Grid infrastructure and enables chemists to utilize Grid resources transparently. Besides, since molecular docking jobs are loosely coupled, we propose to implement the molecular docking job decomposition and generate the sub-jobs to perform in parallel.Due to the existing grid load balancing mechanisms are different, we design and implement a load balancing mechanism that can run in heterogeneous gird environment, to make the sub-jobs execute in parallel to improve the efficiency of molecular docking. What’s more, we provide a molecular docking job editor environment and a unified user data management space, to help chemists conveniently docking on the grid and speed up the process of drug discovery.