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High-throughput molecular dynamics: the powerful new tool for drug discovery
Matthew J Harvey1, Gianni De Fabritiis
1High Performance Computing Service, Imperial College London, South Kensington, London SW7 2AZ, UK.
Drug Discovery Today
|April 17, 2012
Summary
Molecular dynamics simulations, crucial for drug discovery, are now more accessible due to reduced costs from hardware innovations. This makes them a key technology for understanding molecular interactions and predicting drug efficacy.
Area of Science:
- Computational chemistry and biophysics.
- Pharmacology and drug discovery.
Background:
- Molecular dynamics (MD) simulations offer high accuracy for molecular recognition.
- Current limitations are perceived as timescale accessibility, not computational cost.
Purpose of the Study:
- To re-evaluate the primary limitations of molecular dynamics simulations.
- To highlight the potential of MD simulations in modern drug discovery.
Main Methods:
- Analysis of hardware and power cost trends in computational simulations.
- Review of innovations in accelerator processors and high-throughput computing protocols.
Main Results:
- High hardware and energy costs, not simulation timescales, are the main constraints for MD.
- Significant cost reductions in MD sampling have been achieved through technological advancements.
Conclusions:
- Molecular dynamics simulations are now cost-effective for extensive sampling.
- MD simulations are poised to become a pivotal tool for in silico drug discovery, aiding in the analysis of binding pathways, poses, kinetics, and affinities.
