Massive-Scale Binding Free Energy Simulations of HIV Integrase Complexes Using Asynchronous Replica Exchange Framework Implemented on the IBM WCG Distributed Network.

ABSTRACT: To perform massive-scale replica exchange molecular dynamics (REMD) simulations for calculating binding free energies of protein-ligand complexes, we implemented the asynchronous replica exchange (AsyncRE) framework of the binding energy distribution analysis method (BEDAM) in implicit solvent on the IBM World Community Grid (WCG) and optimized the simulation parameters to reduce the overhead and improve the prediction power of the WCG AsyncRE simulations. We also performed the first massive-scale binding free energy calculations using the WCG distributed computing grid and 301 ligands from the SAMPL4 challenge for large-scale binding free energy predictions of HIV-1 integrase complexes. In total there are ∼10000 simulated complexes, ∼1 million replicas, and ∼2000 μs of aggregated MD simul

SUBMITTER: Xia J 

PROVIDER: S-EPMC6496938 | biostudies-literature | 2019 Apr

REPOSITORIES: biostudies-literature