NDLI: FPGA accelerator for protein structure prediction algorithm

Content Provider	IEEE Xplore Digital Library
Author	Jain, A. Gambhir, P. Jindal, P. Balakrishnan, M. Paul, K.
Copyright Year	2009
Description	Author affiliation: Department of Computer Science and Engineering, Indian Institute of Technology, New Delhi, India-110016 (Gambhir, P.; Jindal, P.; Balakrishnan, M.; Paul, K.)
Abstract	Bioinformatics applications are computationally very expensive programs. They work with large data sets and also consume a lot of CPU cycles and often require high degrees of precision. An important application in this area is tertiary structure prediction of proteins. This paper reports a codesign methodology to build hardware accelerators to minimize the running time of a protein energy minimization algorithm. It has been shown that significant speedups can be obtained by moving core time consuming functions onto an FPGA. It has been shown that a 5 fold decrease in the run time of the application can be achieved by simply moving one core function into hardware. Upto an order of magnitude improvement in runtimes can be obtained by moving two functions (core functions in many other bioinformatics applications) which consume 99% of the CPU cycles in the chosen application. A generalized speedup analysis using single and multiple FPGA cards has also been presented.
Starting Page	123
Ending Page	128
File Size	545259
Page Count	6
File Format	PDF
ISBN	9781424438471
DOI	10.1109/SPL.2009.4914901
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2009-04-01
Publisher Place	Brazil
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Protein engineering Minimization methods Computer applications Parallel processing Prediction algorithms Amino acids Hardware Application software Bioinformatics Field programmable gate arrays
Content Type	Text
Resource Type	Article

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1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
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3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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