title: Docking optimization, variance and promiscuity for large-scale drug-like chemical space using high performance computing architectures.
abstract: There is a continuing need to hasten and improve protein-ligand docking to facilitate the next generation of drug discovery. As the drug-like chemical space reaches into the billions of molecules, increasingly powerful computer systems are required to probe, as well as tackle, the software engineering challenges needed to adapt existing docking programs to use next-generation massively parallel processing systems. We demonstrate docking setup using the wrapper code approach to optimize the DOCK program for large-scale computation as well as docking analysis using variance and promiscuity as examples. Wrappers provide faster docking speeds when compared with the naive multi-threading system MPI-DOCK, making future endeavors in large-scale docking more feasible; in addition, eliminating highly variant or promiscuous compounds will make databases more useful.
authors.affiliation: Department of Drug Discovery and Biomedical Sciences, Medical University of South Carolina, 280 Calhoun St, Charleston, SC 29425, USA.
authors.forename: Richard E
authors.initials: RE
authors.lastname: Trager
authors.affiliation: Department of Electrical Engineering and Computer Science, University of Tennessee, 1520 Middle Dr, Knoxville, TN 37996, USA.
authors.forename: Paul
authors.initials: P
authors.lastname: Giblock
authors.affiliation: South Carolina Center for Therapeutic Discovery and Development, Medical University of South Carolina, 280 Calhoun St, Charleston, SC 29425, USA.
authors.forename: Sherwin
authors.initials: S
authors.lastname: Soltani
authors.affiliation: Genomics Sciences and Technology Department, University of Tennessee, 1520 Middle Dr, Knoxville, TN 37996, USA.
authors.forename: Amit A
authors.initials: AA
authors.lastname: Upadhyay
authors.affiliation: Department of Electrical Engineering and Computer Science, University of Tennessee, 1520 Middle Dr, Knoxville, TN 37996, USA; BioTeam Inc., 7 Derosier Drive, Middleton, MA 01949, USA. Electronic address: bhanu@bioteam.net.
authors.forename: Bhanu
authors.initials: B
authors.lastname: Rekapalli
authors.affiliation: Department of Drug Discovery and Biomedical Sciences, Medical University of South Carolina, 280 Calhoun St, Charleston, SC 29425, USA; South Carolina Center for Therapeutic Discovery and Development, Medical University of South Carolina, 280 Calhoun St, Charleston, SC 29425, USA. Electronic address: petersy@musc.edu.
authors.forename: Yuri K
authors.initials: YK
authors.lastname: Peterson
mesh_terms: D003205:Computing Methodologies; D055808:Drug Discovery; D006801:Humans; D062105:Molecular Docking Simulation