Virtual docking is a computational process that aims at predicting the bound conformation of a protein-ligand complex and how well it binds through a scoring algorithm. The scoring functions commonly used in docking applications use significant approximations to rapidly estimate protein-ligand binding affinities and the resulting computational efficiency make these applications useful for virtual high-throughput screens in which millions of molecules can be tested quickly. Most of the screening applications developed to date focus on docking a library of drug-like molecules into one protein target. However, inverse techniques of docking libraries of chemical compounds into a library of proteins are of significant interest, as these permit the investigation of many conformational states of a single protein thus increasing the chemical diversity of drug candidates, and of the effects of a single target compound against a range of different proteins permitting the exploration of toxicity/side-effects of the drug and polypharmacology capabilities. VinaMPI, a massively parallel Message Passing Interface (MPI) and muti-threaded version of the virtual docking program Autodock Vina has been developed. MPI is used to distribute tasks while multi-threading is used to speed-up individual docking tasks. VinaMPI uses a distribution scheme in which tasks are evenly distributed to the workers based on the complexity of each task, as defined by the number of rotatable bonds in each chemical compound investigated. VinaMPI efficiently handles multiple proteins in a ligand screen, allowing for high-throughput inverse docking that presents new opportunities for improving the efficiency of the drug discovery pipeline. VinaMPI successfully ran on 84,672 cores with a continual decrease in job completion time with increasing core count. The ratio of the number of tasks in a screening to the number of workers should be at least around 100 in order to have a good load balance and an optimal job completion time.

Multireceptor high-throughput virtual docking on supercomputers with VinaMPI

246th National Meeting (2013)

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