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

G. Giupponi, M.J. Harvey, G. De Fabritiis
2008 Drug Discovery Today  
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 accelerator processors can deliver over an order of magnitude more floatingpoint operations per second (flops) than standard processors, broadly equivalent to a decade
more » ... f Moore's law growth, and significantly reduce the cost of current atombased molecular simulations. In conjunction with distributed and grid computing solutions, accelerated molecular simulations may finally be used to extend current in silico protocols by 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. Teaser phrase: New accelerated computing devices will unleash the predictive power of molecular modeling and simulation for biotechnology. In light of the significant changes that have occurred lately in microprocessor design, we review the first cost-effective accelerator processors (APs) -the Cell processor and Nvidia graphics processing units (GPUs) -and examine results of their early adoption in stand-alone and grid-computing scenarios in the context of high-throughput molecular simulation for biomolecular applications. Accelerator processors Historically, microprocessor performance has improved primarily through the raising of clock speeds, made possible by the development of ever-finer fabri-
doi:10.1016/j.drudis.2008.08.001 pmid:18762274 fatcat:4lfl77txobdwxd6xnv32qbcwta