FUGUE is a program for recognizing distant homologues by sequence-structure comparison. It utilizes environment-specific substitution tables and structure-dependent gap penalties, where scores for amino acid matching and insertions/deletions are evaluated depending on the local environment of each amino acid residue in a known structure. Given a query sequence (or a sequence alignment), FUGUE scans a database of structural profiles, calculates the sequence-structure compatibility scores and produces a list of potential homologues and alignments.
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J. Shi, T. L. Blundell, and K. Mizuguchi (2001).
FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure- dependent gap penalties.
J. Mol. Biol., 310, 243-257.