Design of a grid service-based platform for in silico protein-ligand screenings

  • Authors:

  • Marshall J. Levesque;Kohei Ichikawa;Susumu Date;Jason H. Haga

  • Affiliations:

  • Department of Bioengineering, University of California, San Diego, 9500 Gilman Dr, La Jolla, CA 92093-0435, United States;Research Center of Socionetwork Strategies, The Institution of Economic and Political Studies, Kansai University, 3-3-35 Yamate-cho, Suita, Osaka 564-8680, Japan;Cybermedia Center, Osaka University, 5-1 Mihogaoka Ibaraki, Osaka 567-0047, Japan;Department of Bioengineering, University of California, San Diego, 9500 Gilman Dr, La Jolla, CA 92093-0435, United States

  • Venue:
  • Computer Methods and Programs in Biomedicine
  • Year:
  • 2009

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Abstract

Grid computing offers the powerful alternative of sharing resources on a worldwide scale, across different institutions to run computationally intensive, scientific applications without the need for a centralized supercomputer. Much effort has been put into development of software that deploys legacy applications on a grid-based infrastructure and efficiently uses available resources. One field that can benefit greatly from the use of grid resources is that of drug discovery since molecular docking simulations are an integral part of the discovery process. In this paper, we present a scalable, reusable platform to choreograph large virtual screening experiments over a computational grid using the molecular docking simulation software DOCK. Software components are applied on multiple levels to create automated workflows consisting of input data delivery, job scheduling, status query, and collection of output to be displayed in a manageable fashion for further analysis. This was achieved using Opal OP to wrap the DOCK application as a grid service and PERL for data manipulation purposes, alleviating the requirement for extensive knowledge of grid infrastructure. With the platform in place, a screening of the ZINC 2,066,906 compound ''drug-like'' subset database against an enzyme's catalytic site was successfully performed using the MPI version of DOCK 5.4 on the PRAGMA grid testbed. The screening required 11.56 days laboratory time and utilized 200 processors over 7 clusters.