Efficient Large-Scale Virtual Screening Based on Heterogeneous Many-Core Supercomputing System.

Abstract

With the rapid growth of virtual drug data- bases, the need for efficient molecular docking tools for large-scale screening is also growing. We have developed Vina@QNLM 2.0, a novel molecular docking system that leverages the logical processing units and computational processing arrays of heterogeneous multicore architecture processors. Compared to Vina@QNLM, the new version optimizes the docking speed without sacrificing accuracy. This greatly improves the scoring capability for large molecules (molecular weight > 500). Simultaneously, the new system provides enhanced support for applications such as reverse target finding through an improved parallel strategy. Vina@QNLM 2.0 achieves a speedup 20 times higher than that, using logical processing units only during a single docking process. Additionally, we successfully scaled the reverse target finding a task to 122,401 kernel groups with a robust scalability of 80.01%. In practice, we completed a reverse target-seeking for nine glycan molecules with 10,094 proteins within 1 hour.