A coprocessor architecture for fast protein structure prediction

Rahim Khoja, Mehul Marolia, Tinku Acharya, Chaitali Chakrabarti

Research output: Contribution to journalArticle

2 Scopus citations

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.

Original languageEnglish (US)
Pages (from-to)2494-2505
Number of pages12
JournalPattern Recognition
Volume39
Issue number12
DOIs
StatePublished - Dec 1 2006

Keywords

  • Neural network
  • PSI BLAST
  • PSIPRED
  • Protein structure prediction
  • VLSI architecture

ASJC Scopus subject areas

  • Software
  • Signal Processing
  • Computer Vision and Pattern Recognition
  • Artificial Intelligence

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