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The impact of accelerator processors for high-throughput molecular modeling and simulation
G Giupponi1, M J Harvey, G De Fabritiis
1Computational Biochemistry and Biophysics Lab, GRID IMIM Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB), C/ Doctor Aiguader 88, 08003 Barcelona, Spain. giovanni.giupponi@upf.edu
Drug Discovery Today
|September 3, 2008
Summary
Cost-effective accelerator processors (APs), like GPUs, significantly boost molecular simulations for biotechnology. This innovation enables faster, more accurate in silico drug discovery by simulating complex protein-ligand interactions.
Area of Science:
- Computational chemistry
- Biotechnology
- High-performance computing
Background:
- Atomistic molecular modeling and simulation are vital for biotechnology.
- Traditional simulations are computationally intensive and costly.
- Advancements in processor technology are needed to enhance simulation capabilities.
Purpose of the Study:
- To evaluate the impact of cost-effective accelerator processors (APs) on molecular modeling and simulation.
- To explore the potential of APs in advancing in silico drug discovery workflows.
- To demonstrate how APs can enable more accurate and extensive molecular simulations.
Main Methods:
- Utilizing accelerator processors (APs) such as IBM Cell and Nvidia GPUs.
- Implementing distributed and grid-computing solutions.
- Performing atomistic molecular simulations with enhanced computational power.
Main Results:
- APs provide over an order of magnitude increase in floating-point operations per second (flops) compared to standard processors.
- Significant cost reduction for current atom-based molecular simulations.
- Enabling simulations of hundreds of protein-ligand complexes with full molecular specificity.
Conclusions:
- APs represent a significant technological innovation for the biotechnology industry.
- Accelerated molecular simulations can extend in silico protocols with accurate thermodynamic calculations.
- This advancement is crucial for in silico drug discovery, allowing for more precise and comprehensive analysis.
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