title: Molecular dynamics-based virtual screening: accelerating the drug discovery process by high-performance computing.
abstract: 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.
authors.affiliation: School of Pharmaceutical Sciences & Institute of Human Virology, Sun Yat-Sen University , 132 East Circle Road at University City, Guangzhou 510006, China.
authors.forename: Hu
authors.initials: H
authors.lastname: Ge
authors.forename: Yu
authors.initials: Y
authors.lastname: Wang
authors.forename: Chanjuan
authors.initials: C
authors.lastname: Li
authors.forename: Nanhao
authors.initials: N
authors.lastname: Chen
authors.forename: Yufang
authors.initials: Y
authors.lastname: Xie
authors.forename: Mengyan
authors.initials: M
authors.lastname: Xu
authors.forename: Yingyan
authors.initials: Y
authors.lastname: He
authors.forename: Xinchun
authors.initials: X
authors.lastname: Gu
authors.forename: Ruibo
authors.initials: R
authors.lastname: Wu
authors.forename: Qiong
authors.initials: Q
authors.lastname: Gu
authors.forename: Liang
authors.initials: L
authors.lastname: Zeng
authors.forename: Jun
authors.initials: J
authors.lastname: Xu
mesh_terms: D000465:Algorithms; D001185:Artificial Intelligence; D001665:Binding Sites; D062126:Databases, Chemical; D030562:Databases, Protein; D055808:Drug Discovery; D016333:HIV Protease / Q000737:chemistry*; D017320:HIV Protease Inhibitors / Q000737:chemistry*; D057166:High-Throughput Screening Assays / Q000191:economics / Q000295:instrumentation; D006801:Humans; D008024:Ligands; D062105:Molecular Docking Simulation; D056004:Molecular Dynamics Simulation; D009439:Neuraminidase / Q000037:antagonists & inhibitors / Q000737:chemistry*; D047493:PPAR alpha / Q000037:antagonists & inhibitors / Q000737:chemistry*; D011485:Protein Binding; D054852:Small Molecule Libraries / Q000737:chemistry*; D013329:Structure-Activity Relationship; D013816:Thermodynamics; D014584:User-Computer Interface
chemical_list: D017320:HIV Protease Inhibitors; D008024:Ligands; D047493:PPAR alpha; D054852:Small Molecule Libraries; D009439:Neuraminidase; D016333:HIV Protease