Processors White Papers
Molecular Fingerprinting on the SIMD Parallel Processor Kestrel
Overview In combinatorial library design and use, the conformation space of molecules can be represented using three-dimensional (3-D) pharmacophores. For large libraries of exible molecules, the calculation of these 3-D pharmacophoric fingerprints can require examination of trillions of pharmacophores, presenting a significant practical challenge. Here it describes 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.
| Publisher | Stanford Knowledgebase | File Format | PDF, requires Acrobat Rdr 5 |
|---|---|---|---|
| Date Published | June 2001 | Downloads | 71 |
| Format | White Papers | ||
| Topics | |||
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