title: Accelerating molecular docking calculations using graphics processing units.
abstract: The generation of molecular conformations and the evaluation of interaction potentials are common tasks in molecular modeling applications, particularly in protein-ligand or protein-protein docking programs. In this work, we present a GPU-accelerated approach capable of speeding up these tasks considerably. For the evaluation of interaction potentials in the context of rigid protein-protein docking, the GPU-accelerated approach reached speedup factors of up to over 50 compared to an optimized CPU-based implementation. Treating the ligand and donor groups in the protein binding site as flexible, speedup factors of up to 16 can be observed in the evaluation of protein-ligand interaction potentials. Additionally, we introduce a parallel version of our protein-ligand docking algorithm PLANTS that can take advantage of this GPU-accelerated scoring function evaluation. We compared the GPU-accelerated parallel version to the same algorithm running on the CPU and also to the highly optimized sequential CPU-based version. In terms of dependence of the ligand size and the number of rotatable bonds, speedup factors of up to 10 and 7, respectively, can be observed. Finally, a fitness landscape analysis in the context of rigid protein-protein docking was performed. Using a systematic grid-based search methodology, the GPU-accelerated version outperformed the CPU-based version with speedup factors of up to 60.
authors: Cambridge Crystallographic Data Centre, CB21EZ Cambridge, United Kingdom. korb@ccdc.cam.ac.uk
authors: Oliver
authors: O
authors: Korb
authors: Thomas
authors: T
authors: Stützle
authors: Thomas E
authors: TE
authors: Exner
mesh_terms: D000465:Algorithms; D001665:Binding Sites; D003198:Computer Simulation; D003201:Computers; D015195:Drug Design; D008024:Ligands; D008958:Models, Molecular; D008968:Molecular Conformation; D011485:Protein Binding; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D012984:Software
chemical_list: D008024:Ligands; D011506:Proteins