Toward Fast and Accurate Binding Affinity Prediction with pmemdGTI: An Efficient Implementation of GPU-Accelerated Thermodynamic Integration

Journal of Chemical Theory and Computation vol. 13  p. 3077-3084  DOI: 10.1021/acs.jctc.7b00102
PMID/PMCID: PMC5843186 Published: 2017-07-05 

Tai-Sung Lee [ ] , Yuan Hu, Brad Sherborne, Zhuyan Guo, Darrin M. York [ ]

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We report the implementation of the thermodynamic integration method on the pmemd module of the AMBER 16 package on GPUs (pmemdGTI). The pmemdGTI code typically delivers over 2 orders of magnitude of speed-up relative to a single CPU core for the calculation of ligand-protein binding affinities with no statistically significant numerical differences and thus provides a powerful new tool for drug discovery applications.