NDLI: Protein Structure Prediction on GPU: A Declarative Approach in a Multi-agent Framework

Content Provider	IEEE Xplore Digital Library
Author	Campeotto, F. Dovier, A. Pontelli, E.
Copyright Year	2013
Description	Author affiliation: New Mexico State Univ., Las Cruces, NM, USA (Campeotto, F.; Pontelli, E.) \|\| DIMI, Univ. of Udine, Udine, Italy (Dovier, A.)
Abstract	This paper provides a novel perspective in the Protein Structure Prediction (PSP) problem. The PSP problem focuses on determining putative 3D structures of a protein starting from its primary sequence. The proposed approach relies on a multi-agents approach, where concurrent agents explore the folding of different parts of a protein. The strength of the approach lies in the agents' ability to apply different types of knowledge (expressed in the form of declarative constraints) to prune the local space of folding alternatives. The paper demonstrates the suitability of a GPU approach to implement such multi-agent infrastructure, with significant improvements in speed and quality of solutions w.r.t. other methods (e.g., based on fragments assembly approaches).
Starting Page	474
Ending Page	479
File Size	706212
Page Count	6
File Format	PDF
ISBN	9780769551173
ISSN	01903918
DOI	10.1109/ICPP.2013.57
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2013-10-01
Publisher Place	France
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Proteins Graphics processing units Amino acids Instruction sets Kernel Periodic structures Arrays Protein Structure Prediction GPU Constraint Programming
Content Type	Text
Resource Type	Article

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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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