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Can we trust docking results?
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243rd ACS
Mar 25-29, 2012
San Diego, CA
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Presentation at the:  Spring 2009 ACS National Meeting & Exposition


to be held in Salt Lake City, UT, Mar 22 - 26, 2009



Presentation in COMP 1,

SESSION: Advancing Computational Chemistry through High-Performance Computing: From the Workstation to Petascale and Beyond: Michael Dewar Memorial Symposium

Sunday, March 22, 2009 from 8:30 AM to 9:10 AM

Docking performance accelerated 30-50 fold on the Cell/BE processor

Zsolt Zsoldos 
SimBioSys Inc., 135 Queen's Plate Dr, Unit 520, Toronto, ON M9W 6V1, Canada

Abstract:

The eHiTS flexible docking has proven to be among the most accurate pose prediction tools (http://www.simbiosys.com/ehits/ehits_validation.html) providing one of the highest enrichment factors based on comparative evaluation studies (http://www.simbiosys.com/ehits/ehits_enrichment.html). The accurate results of eHiTS have been achieved at the price of longer CPU times in the past, but that has changed with the recent port of the algorithm to the Cell/BE processor (http://www.bio-itworld.com/issues/2008/july-august/simbiosys.html). The revolutionary hardware that powers RoadRunner (the world's current fastest supercomputer) and also available in the low cost SONY PS3 game console, gives eHiTS 30-50 fold speedup compared to a single core Intel/AMD processor. The advantages of the Cell/BE platform over other acceleration techniques (FPGA,GPGPU) will be described, along with the challenges faced during the porting effort. A new proximity data structure is introduced that is optimized for SIMD architectures. It allows efficient evaluation of short range pairwise interactions with optimum cache locality.


Full Presentation

Back to the other SimBioSys related 
Spring ACS, 2009 presentations:

[1], [2], [3], [4], [5], [6]. [7]

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