From fold recognition to flexible docking
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comprises an environment-specific substitution table that takes into account secondary structure, solvent accessibility and hydrogen-bonding interactions, and structure-dependent gap penalties. These tables are derived from the structural alignments of experimentally determined protein structures in HOMSTRADTM 2 — a database containing thousands of 3D protein structures clustered into related families. The key elements of FUGUE are environment-specific substitution tables, structure-dependent gap penalties, automated alignment method selection, and HOMSTRAD.
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