Molecular Dynamics-Based Virtual Screening: Accelerating the Drug Discovery Process by High-Performance Computing

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• 作者：Hu Ge ; Yu Wang ; Chanjuan Li ; Nanhao Chen ; Yufang Xie ; Mengyan Xu ; Yingyan He ; Xinchun Gu ; Ruibo Wu ; Qiong Gu ; Liang Zeng ; Jun Xu
• 刊名：Journal of Chemical Information and Modeling
• 出版年：2013
• 出版时间：October 28, 2013
• 年：2013
• 卷：53
• 期：10
• 页码：2757-2764
• 全文大小：530K
• 年卷期：v.53,no.10(October 28, 2013)
• ISSN：1549-960X

文摘

High-performance computing (HPC) has become a state strategic technology in a number of countries. One hypothesis is that HPC can accelerate biopharmaceutical innovation. Our experimental data demonstrate that HPC can significantly accelerate biopharmaceutical innovation by employing molecular dynamics-based virtual screening (MDVS). Without using HPC, MDVS for a 10K compound library with tens of nanoseconds of MD simulations requires years of computer time. In contrast, a state of the art HPC can be 600 times faster than an eight-core PC server is in screening a typical drug target (which contains about 40K atoms). Also, careful design of the GPU/CPU architecture can reduce the HPC costs. However, the communication cost of parallel computing is a bottleneck that acts as the main limit of further virtual screening improvements for drug innovations.