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

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.