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The impact of accelerator processors for high-throughput molecular modeling and simulation

G. Giupponi, M. Harvey, G. Defabritiis
Computational Biochemistry and Biophysics Lab, GRID IMIM Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB), C/ Doctor Aiguader 88, 08003 Barcelona, Spain
Drug Discovery Today, Vol. 13, No. 23-24. (16 December 2008), pp. 1052-1058

@article{giupponi2008impact,

   title={The impact of accelerator processors for high-throughput molecular modeling and simulation},

   author={Giupponi, G. and Harvey, MJ and De Fabritiis, G.},

   journal={Drug discovery today},

   volume={13},

   number={23-24},

   pages={1052–1058},

   issn={1359-6446},

   year={2008},

   publisher={Elsevier}

}

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The recent introduction of cost-effective accelerator processors (APs), such as the IBM Cell processor and Nvidia’s graphics processing units (GPUs), represents an important technological innovation which promises to unleash the full potential of atomistic molecular modeling and simulation for the biotechnology industry. Present APs can deliver over an order of magnitude more floating-point operations per second (flops) than standard processors, broadly equivalent to a decade of Moore’s law growth, and significantly reduce the cost of current atom-based molecular simulations. In conjunction with distributed and grid-computing solutions, accelerated molecular simulations may finally be used to extend current in silico protocols by the use of accurate thermodynamic calculations instead of approximate methods and simulate hundreds of protein-ligand complexes with full molecular specificity, a crucial requirement of in silico drug discovery workflows.
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