VinaMPI: Facilitating multiple receptor high-throughput virtual docking on high-performance computers

Abstract

The program VinaMPI has been developed to enable massively large virtual drug screens on leadership-class computing resources, using a large number of cores to decrease the time-to-completion of the screen. VinaMPI is a massively parallel Message Passing Interface (MPI) program based on the multithreaded virtual docking program AutodockVina, and is used to distribute tasks while multithreading 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. The code is freely available and downloadable. Instructions for downloading and using the code are provided in the Supporting Information.

Ensemble-based docking: From hit discovery to metabolism and toxicity predictions

“…To enable docking on supercomputers we have developed the program VinaMPI, 12 an MPI parallelization of the AutodockVina program, 11 that scales on tens of thousands of supercomputer cores. This parallelization addresses several key points needed for efficient docking on supercomputers: the handling of an even distribution of work by the computing cores, the handling of communication between cores—including handling of failing cores, and, importantly, the inclusion of the complexity of a given docking calculation in the prioritization and distribution of computing tasks.…”

“…Olson laboratory, The Scripps Research Institute, San Diego, California). 11 We used Autodock Vina both in its native distribution and in a parallelized version, called VinaMPI, developed by our laboratories 12 and described below. The MOE program was used in the metabolic activation estrogenization pathway project described here, the Autodock Vina was used in the hit discovery project on modulatoes of coagulation, and the VinaMPI program was used in the toxicity prediction project.…”

Virtual screening: An in silico tool for interlacing the chemical universe with the proteome

“…While INVDOCK [89], FlexX [90], and GOLD [91] require a license, programs like VinaMPI (Autodock) [92] and others listed in the Supporting information are free. In particular, in Table 1 of the Supporting information, we provide details on accessible softwares for VS/IVS regarding the docking engines, the results, cluster/workstation/web, the operating system, the availability and application examples.…”

“…The next application shows how using different IVS protocols can yield pharmacologically more relevant targets for compounds such as catechins, which are known to be rather promiscuous in terms of binding to proteins. The authors used two different docking programs, Autodock [92,183,184] and Tarfisdock [163], for docking the catechins into the PDTD protein database [172]. The aim was to discover potential antineoplastic targets of the tea functional components epigallocatechin gallate (EGCG), epigallocatechin, epicatechin gallate and epicatechin.…”

Open source molecular modeling

“…VinaMPI [175] is a wrapper for AutoDock Vina that uses OpenMPI to run large-scale virtual screens on a computing cluster.…”