• DocumentCode
    527935
  • Title

    FPGA-based acceleration of the AutoDock molecular docking software

  • Author

    Pechan, Imre ; Fehér, Béla ; Bérces, Attila

  • Author_Institution
    Dept. of Meas. & Inf. Syst., Budapest Univ. of Technol. & Econ., Budapest, Hungary
  • fYear
    2010
  • fDate
    18-21 July 2010
  • Firstpage
    1
  • Lastpage
    4
  • Abstract
    AutoDock is a popular software for the bioinformatics related molecular docking problem. The FPGA-based acceleration of AutoDock is presented and evaluated in this paper. The implementation applies pipelines and fine-grained parallelization, and achieves a ×10-40 speedup over a 3.2 GHz CPU. Test runs show that the overall accuracy of the algorithm was preserved despite the slight modifications of the original method and the fixed-point arithmetic used in the FPGA.
  • Keywords
    bioinformatics; field programmable gate arrays; fixed point arithmetic; molecular biophysics; parallel processing; AutoDock molecular docking software; FPGA-based acceleration; bioinformatics; fine-grained parallelization; fixed-point arithmetic; related molecular docking problem; Atomic clocks; Field programmable gate arrays; Pipelines; Prediction algorithms; Random access memory; Search methods; AutoDock; FPGA; bioinformatics; hardware acceleration; molecular docking;
  • fLanguage
    English
  • Publisher
    ieee
  • Conference_Titel
    Ph.D. Research in Microelectronics and Electronics (PRIME), 2010 Conference on
  • Conference_Location
    Berlin
  • Print_ISBN
    978-1-4244-7905-4
  • Type

    conf

  • Filename
    5587139
    • Link To Document
    https://search.isc.ac/dl/search/defaultta.aspx?DTC=49&DC=527935