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Molecular fingerprinting on the SIMD parallel processor Kestrel.

E Rice1, R Hughey

  • 1Department of Computer Engineering, University of California, Santa Cruz, CA 95064, USA. elrice@cse.ucsc.edu

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing
|March 27, 2001
PubMed
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Calculating three-dimensional (3-D) pharmacophores for large molecular libraries is computationally intensive. This study mapped the problem to a parallel processor, achieving a significant speedup for 3-D pharmacophore fingerprint analysis.

Area of Science:

  • Computational chemistry
  • Bioinformatics
  • Computer science

Background:

  • Three-dimensional (3-D) pharmacophores are crucial for representing molecular conformation space in combinatorial library design.
  • Calculating 3-D pharmacophoric fingerprints for large, flexible molecular libraries involves examining trillions of conformations, posing a significant computational challenge.

Purpose of the Study:

  • To address the computational challenge of calculating 3-D pharmacophoric fingerprints for large molecular libraries.
  • To demonstrate the effectiveness of parallel processing for accelerating this computation.

Main Methods:

  • The problem of calculating 3-D pharmacophoric fingerprints was mapped to the UCSC Kestrel parallel processor, a single-instruction multiple-data (SIMD) architecture.
  • Data parallelism was achieved by processing multiple molecular conformations simultaneously and by optimizing the representation of fingerprint structures within the processor's arrays.

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Main Results:

  • The developed application achieved a speedup exceeding 35 times compared to an SGI 2000 processor.
  • The use of the Kestrel parallel processor significantly reduced the time required for 3-D pharmacophore calculations.

Conclusions:

  • Mapping 3-D pharmacophore calculations to parallel processors like UCSC Kestrel offers a practical solution for handling large molecular libraries.
  • This approach demonstrates substantial performance gains, making complex molecular analyses more feasible.