FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties.

@article{Shi2001FUGUESH,
  title={FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties.},
  author={Jiye Shi and Tom L. Blundell and K. Mizuguchi},
  journal={Journal of molecular biology},
  year={2001},
  volume={310 1},
  pages={243-57}
}
FUGUE, a program for recognizing distant homologues by sequence-structure comparison (http://www-cryst.bioc.cam.ac.uk/fugue/), has three key features. (1) Improved environment-specific substitution tables. Substitutions of an amino acid in a protein structure are constrained by its local structural environment, which can be defined in terms of secondary structure, solvent accessibility, and hydrogen bonding status. The environment-specific substitution tables have been derived from structural… CONTINUE READING
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