PROTEAN: Deriving Protein Structure from Constraints

Barbara Hayes-Roth, Bruce Buchanan, Olivier Lichtarge, Mike Hewitt, Russ Altman, James Brinkley, Craig Cornelius, Bruce Duncan, Oleg Jardetzky

PROTEAN is an evolving knowledge-based system that is intended to identify the three-dimensional conformations of proteins in solution. Using a variety of empirically derived constraints, PROTEAN must identify legal positions for each of a protein’s constituent structures (e.g., atoms, amino acids, helices) in three-dimensional space. In fact, because protein-structure analysis is an underconstrained problem, PROTEAN must identify the entire family of conformations allowed by available constraints. In this paper, we discuss PROTEAN’s approach to the protein-structure analysis problem and its current implementation within the BBl blackboard architecture.

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