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)


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.


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.


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 1.
    Chen, R., Weng, Z.: A novel shape complementarity scoring function for proteinprotein docking. Proteins 51, 397–408 (2003)CrossRefGoogle Scholar
  2. 2.
    Wriggers, W., Milligan, R., McCammon, J.: Situs: A package for docking crystal structures into low resolution maps. J. Struct. Biol. 125, 185–195 (1999)CrossRefGoogle Scholar
  3. 3.
    Chen, R., Weng, Z.: Docking unbound proteins using shape complementarity, desolvation, and electrostatics. Proteins 47, 281–294 (2002)CrossRefGoogle Scholar
  4. 4.
    Katchalski-Katzir, E., Shariv, I., Eisenstein, M., Freeman, A., Aflalo, C., Vasker, I.: Molecular surface recognition: Determination of geometric fit between prtoeins and their ligands by correlation techniques. PNAS 89, 2195–2199 (1992)CrossRefGoogle Scholar
  5. 5.
    Swartzlander, E.: Systolic Signal Processing Systems. Marcel Drekker, Inc., New York (1987)Google Scholar
  6. 6.
    Berman, H., et al.: The protein data bank. Nucl. Acids Res. 28, 235–242 (2000)CrossRefGoogle Scholar
  7. 7.
    Press, W., Teukolsky, S., Vetterling, W., Flannery, B.: Numerical Recipes in C: The Art of Scientific Computing. Cambridge University Press, Cambridge (1992)Google Scholar

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

Personalised recommendations