Molecular fingerprinting on the SIMD parallel processor Kestrel.
In combinatorial library design and use, the conformation space of molecules can be represented using three-dimensional (3-D) pharmacophores. For large libraries of flexible molecules, the calculation of these 3-D pharmacophoric fingerprints can require examination of trillions of pharmacophores, presenting a significant practical challenge. Here we describe the mapping of this problem to the UCSC Kestrel parallel processor, a single-instruction multiple-data (SIMD) processor. Data parallelism is achieved by simultaneous processing of multiple conformations and by careful representation of the fingerprint structure in the array. The resulting application achieved a 35+ speedup over an SGI 2000 processor on the prototype Kestrel board.
Department of Computer Engineering, University of California, Santa Cruz, CA 95064, USA. elrice@cse.ucsc.edu
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D020650:Combinatorial Chemistry Techniques; D003201:Computers; D015195:Drug Design; D008968:Molecular Conformation; D015394:Molecular Structure; D012984:Software