NDLI: A coprocessor architecture for fast protein structure prediction

Content Provider	IEEE Xplore Digital Library
Author	Marolia, M. Khoja, R. Acharya, T. Chakrabarti, C.
Copyright Year	2005
Description	Author affiliation: Dept. of Electr. Eng., Arizona State Univ., Tempe, AZ, USA (Marolia, M.; Khoja, R.; Acharya, T.; Chakrabarti, C.)
Abstract	Predicting protein structure from amino acid sequence is computationally very intensive. In order to speed up protein sequence matching and processing, it is necessary to develop special purpose VLSI architectures that exploit the underlying computational structures. In this paper, we present a coprocessor architecture for fast protein structure prediction based on the PSIPRED algorithm. The architecture consists of systolic arrays to speed up the data intensive sequence alignment and structure prediction steps, and finite state machines for the control dominated steps. The architecture has been synthesized using synopsis DC compiler using 0.18/spl mu/m CMOS technology. The synthesized architecture requires 783,228 units of gate area and 226KB of memory, and can be clocked at 100 MHz. The architecture processes amino acid sequences extremely fast; for a database of 135,000,000 amino acids, the secondary structure of a query sequence of length -150 amino acids can be predicted in -11 seconds.
Starting Page	413
Ending Page	418
File Size	335875
Page Count	6
File Format	PDF
ISBN	0780393333
ISSN	15206130
DOI	10.1109/SIPS.2005.1579904
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2005-11-02
Publisher Place	Greece
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Coprocessors Computer architecture Amino acids CMOS technology Protein sequence Very large scale integration Systolic arrays Automata Clocks Databases
Content Type	Text
Resource Type	Article

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