Genome Science and Technology, University of Tennessee, Knoxville, Tennessee, USA.
J Comput Chem. 2013 Sep 30;34(25):2212-21. doi: 10.1002/jcc.23367.
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.
VinaMPI 程序旨在利用大量核心来减少虚拟药物筛选的完成时间，从而在领导级计算资源上实现大规模的虚拟药物筛选。VinaMPI 是一个基于多线程虚拟对接程序 AutodockVina 的大规模并行消息传递接口（MPI）程序，用于分配任务，同时使用多线程来加快单个对接任务的速度。VinaMPI 使用一种分配方案，根据每个化合物中旋转键的数量来定义每个任务的复杂性，将任务均匀地分配给工人。VinaMPI 有效地处理配体筛选中的多个蛋白质，允许进行高通量的反向对接，为提高药物发现管道的效率提供了新的机会。VinaMPI 成功地在 84672 个核心上运行，随着核心数量的增加，作业完成时间持续减少。为了实现良好的负载平衡和最佳作业完成时间，筛选中任务的数量与工人的数量之比至少应为 100 左右。该代码是免费提供的，可以下载。下载和使用代码的说明在支持信息中提供。
