Summary: The application of docking to large-scale experiments or the explicit treatment of protein flexibility are part of the new challenges in structural bioinformatics that will require large computer resources and more efficient algorithms. Highly optimized fast Fourier transform (FFT) approaches are broadly used in docking programs but their optimal code implementation leaves hardware acceleration as the only option to significantly reduce the computational cost of these tools. In this work we present Cell-Dock, an FFT-based docking algorithm adapted to the Cell BE processor. We show that Cell-Dock runs faster than FTDock with maximum speedups of above 200×, while achieving results of similar quality.
Bibliographical noteFunding Information:
Funding: This work was supported by the Spanish Ministry of Science and Innovation (BIO2010-22324, TIN2006-27664-E, TIN2007-60625 and CSD2007-00050), Generalitat de Catalunya (2009-SGR-980), the European Commission in the context of the EnCORE project (contract number FP7-248647), the HiPEAC2 Network of Excellence (contract number FP7/IST-217068) and the MareIncognito project under the BSC-IBM collaboration agreement.