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Drug Discovery and Molecular Dynamics: Methods, Applications and Perspective Beyond the Second Timescale
Gerard Martínez-Rosell1, Toni Giorgino2, Matt J Harvey3
1Computational Biophysics Laboratory (GRIB-IMIM), Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB), Doctor Aiguader 88, 08003, Barcelona. Spain.
Current Topics in Medicinal Chemistry
|April 18, 2017
Summary
Graphical processing unit (GPU)-accelerated molecular dynamics (MD) simulations are revolutionizing drug discovery. Millisecond timescales are now achievable, positioning GPU-MD as a key tool for academia and industry.
Area of Science:
- Computational Chemistry
- Biophysics
- Pharmacology
Background:
- Graphical processing unit (GPU)-accelerated bio-molecular dynamics (MD) simulations emerged publicly in 2009.
- Significant throughput improvements have enabled millisecond sampling timescales.
Purpose of the Study:
- To review successful applications of GPU-based MD in drug discovery.
- To analyze overcome limitations and discuss remaining challenges in GPU-MD.
Main Methods:
- Review of published literature on GPU-based MD simulations.
- Analysis of application successes and limitations in drug discovery.
Main Results:
- GPU-based MD simulations have expanded to diverse molecular studies.
- Extrapolation suggests millisecond sampling will be standard by 2022, driving adoption in drug discovery.
Conclusions:
- GPU-based MD is poised to become a primary tool in academic and industrial drug discovery.
- Continued advancements will address current limitations and expand future applications.