Mining residue contacts in proteins using local structure predictions

Mohammed J. Zaki, Shan Jin, Chris Bystroff

Research output: Contribution to journalArticle

15 Citations (Scopus)


In this paper we develop data mining techniques to predict three-dimensional (3-D) contact potentials among protein residues (or amino acids) based on the hierarchical nucleation-propagation model of protein folding. We apply a hybrid approach, using a hidden Markov model to extract folding initiation sites, and then apply association mining to discover contact potentials. The new hybrid approach achieves accuracy results better than those reported previously.

Original languageEnglish
Pages (from-to)789-801
Number of pages13
JournalIEEE Transactions on Systems, Man, and Cybernetics, Part B: Cybernetics
Issue number5
Publication statusPublished - 1 Oct 2003



  • Association rules
  • Contact maps
  • Data mining
  • Hidden Markov models
  • Protein structure prediction

ASJC Scopus subject areas

  • Control and Systems Engineering
  • Software
  • Information Systems
  • Human-Computer Interaction
  • Computer Science Applications
  • Electrical and Electronic Engineering

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