PAPER—Accelerating parallel evaluations of ROCS |
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Authors: | Imran S. Haque Vijay S. Pande |
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Affiliation: | 1. Department of Computer Science, Stanford University, Stanford, CA, USA;2. Department of Chemistry, Stanford University, Stanford, CA, USA |
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Abstract: | Modern graphics processing units (GPUs) are flexibly programmable and have peak computational throughput significantly faster than conventional CPUs. Herein, we describe the design and implementation of PAPER, an open‐source implementation of Gaussian molecular shape overlay for NVIDIA GPUs. We demonstrate one to two order‐of‐magnitude speedups on high‐end commodity GPU hardware relative to a reference CPU implementation of the shape overlay algorithm and speedups of over one order of magnitude relative to the commercial OpenEye ROCS package. In addition, we describe errors incurred by approximations used in common implementations of the algorithm. © 2009 Wiley Periodicals, Inc. J Comput Chem 2010 |
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Keywords: | GPU computing ROCS molecular overlay CUDA shape comparison |
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