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FPGA Acceleration of Rigid Molecule Interactions

  • Tom Van Court
  • Yongfeng Gu
  • Martin Herbordt
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3203)

Abstract

Modeling of molecule interactions often uses rigid models and correlation techniques, either in early screening passes or as steps within more complex models. Even rigid models are time-consuming when applied to large models at 103–105 different three-axis rotations. This paper presents an FPGA structure for performing the correlations efficiently using a systolic array for 3-D correlation and an addressing technique for low-overhead rotation of a 3-D voxel models around three axes. We find a 200× speedup in our FPGA implementation compared to the standard transform-based method.

Keywords

Systolic Array FPGA Implementation Rigid Model Voxel Model Shape Complementarity 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2004

Authors and Affiliations

  • Tom Van Court
    • 1
  • Yongfeng Gu
    • 1
  • Martin Herbordt
    • 1
  1. 1.Department of Electrical and Computer EngineeringBoston UniversityBostonUSA

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