Building a Chemical-Protein Interactome on the Open Science Grid

Abstract
The Structural Protein-Ligand Interactome (SPLINTER) project predicts the interaction of thousands of small molecules with thousands of proteins. These interactions are predicted using the three-dimensional structure of the bound complex between each pair of protein and compound that is predicted by molecular docking. These docking runs consist of millions of individual short jobs each lasting only minutes. However, computing resources to execute these jobs (which cumulatively take tens of millions of CPU hours) are not readily or easily available in a cost effective manner. By looking to National Cyberinfrastructure resources, and specifically the Open Science Grid (OSG), we have been able to harness CPU power for researchers at the Indiana University School of Medicine to provide a quick and efficient solution to their unmet computing needs. Using the job submission infrastructure provided by the OSG, the docking data and simulation executable was sent to more than 100 universities and research centers worldwide. These opportunistic resources provided millions of CPU hours in a matter of days, greatly reducing time docking simulation time for the research group. The overall impact of this approach allows researchers to identify small molecule candidates for individual proteins, or new protein targets for existing FDA-approved drugs and biologically active compounds.
Description
Keywords
grid, open, science, protein, Interactome
Citation
Quick, R., S. Meroueh, S. Hayashi, M. Rynge, S. Teige, D. Xu, and B. Wang. Building a Chemical-Protein Interactome on the Open Science Grid. In: Proceedings of International Symposium of Grid and Cloud Computing. (Taipei, Taiwan, 2015) Available from: http://pos.sissa.it/archive/conferences/239/024/ISGC2015_024.pdf
DOI
Relation
Rights
Except where otherwise noted, the contents of this presentation are copyright of the Trustees of Indiana University. This content is released under the Creative Commons Attribution 3.0 Unported license (http://creativecommons.org/licenses/by/3.0/). This license includes the following terms: You are free to share - to copy, distribute and transmit the work and to remix - to adapt the work under the following conditions: attribution - you must attribute the work in the manner specified by the author or licensor (but not in any way that suggests that they endorse you or your use of the work). For any reuse or distribution, you must make clear to others the license terms of this work
Type
Conference paper