title: Fast docking on graphics processing units via Ray-Casting.
abstract: Docking Approach using Ray Casting (DARC) is structure-based computational method for carrying out virtual screening by docking small-molecules into protein surface pockets. In a complementary study we find that DARC can be used to identify known inhibitors from large sets of decoy compounds, and can identify new compounds that are active in biochemical assays. Here, we describe our adaptation of DARC for use on Graphics Processing Units (GPUs), leading to a speedup of approximately 27-fold in typical-use cases over the corresponding calculations carried out using a CPU alone. This dramatic speedup of DARC will enable screening larger compound libraries, screening with more conformations of each compound, and including multiple receptor conformations when screening. We anticipate that all three of these enhanced approaches, which now become tractable, will lead to improved screening results.
authors: Center for Bioinformatics, University of Kansas, Lawrence, Kansas, United States of America.
authors: Karen R
authors: KR
authors: Khar
authors: Lukasz
authors: L
authors: Goldschmidt
authors: John
authors: J
authors: Karanicolas
mesh_terms: D000465:Algorithms; D003196:Computer Graphics; D057166:High-Throughput Screening Assays; D008024:Ligands; D062105:Molecular Docking Simulation; D011485:Protein Binding; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D054852:Small Molecule Libraries / Q000737:chemistry*; D012984:Software
chemical_list: D008024:Ligands; D011506:Proteins; D054852:Small Molecule Libraries
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