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Protein decoy assembly using short fragments under geometric constraints
Author(s) -
Kolodny R.,
Levitt M.
Publication year - 2003
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.10262
Subject(s) - chemistry , decoy , biophysics , crystallography , nanotechnology , biochemistry , receptor , biology , materials science
Abstract 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‐α proteins, and shows promising results for α and β proteins. © 2003 Wiley Periodicals, Inc. Biopolymers 68: 278–285, 2003