Protein decoy assembly using short fragments under geometric constraints

A small set of protein fragments can represent adequately all known local protein structure. This set of fragments, along with a construction scheme that assembles these fragments into structures, defines a discrete (relatively small) conformation space, which approximates protein structures accurately. We generate protein decoys by sampling geometrically valid structures from this conformation space, biased by the secondary structure prediction for the protein. Unlike other methods, secondary structure prediction is the only protein-specific information used for generating the decoys. Nevertheless, these decoys are qualitatively similar to those found by others. The method works well for all-alpha proteins, and shows promising results for alpha and beta proteins. (C) 2003 Wiley Periodicals, Inc.