A coprocessor architecture for fast protein structure prediction

Authors:
Rahim Khoja;Mehul Marolia;Tinku Acharya;Chaitali Chakrabarti
Affiliations:
Department of Electrical Engineering, Arizona State University, Tempe, AZ, USA;Department of Electrical Engineering, Arizona State University, Tempe, AZ, USA;Department of Electrical Engineering, Arizona State University, Tempe, AZ, USA;Department of Electrical Engineering, Arizona State University, Tempe, AZ, USA
Venue:
Pattern Recognition
Year:
2006

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Abstract

Predicting the protein structure from an amino acid sequence is computationally very intensive. In order to speed up protein sequence matching and processing, we present a novel coprocessor architecture for fast protein structure prediction. 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 Synopsys DC Compiler in 0.18 micron CMOS technology and details of its area and timing performance have been provided. A procedure to develop architectures with area-time trade-offs has also been presented.