FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties. 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 alignments in the HOMSTRAD database (http://www-cryst.bioc.cam.ac.uk/homstrad/). (2) Automatic selection of alignment algorithm with detailed structure-dependent gap penalties. FUGUE uses the global-local algorithm to align a sequence-structure pair when they greatly differ in length and uses the global algorithm in other cases. The gap penalty at each position of the structure is determined according to its solvent accessibility, its position relative to the secondary structure elements (SSEs) and the conservation of the SSEs. (3) Combined information from both multiple sequences and multiple structures. FUGUE is designed to align multiple sequences against multiple structures to enrich the conservation/variation information. We demonstrate that the combination of these three key features implemented in FUGUE improves both homology recognition performance and alignment accuracy.

References in zbMATH (referenced in 9 articles )

Showing results 1 to 9 of 9.
Sorted by year (citations)

  1. Carugo, Oliviero (ed.); Eisenhaber, Frank (ed.): Data mining techniques for the life sciences (2016)
  2. Kasabov, Nikola (ed.): Springer handbook of bio-/neuro-informatics (2014)
  3. Durand, Pierre M.; Hazelhurst, Scott; Coetzer, Theresa L.: Evolutionary rates at codon sites May be used to align sequences and infer protein domain function (2010) ioport
  4. Łukasiak, Piotr; Błażewicz, Jacek; Miłostan, Maciej: Some operations research methods for analyzing protein sequences and structures (2010)
  5. Zhang, Ning; Duan, Guangyou; Gao, Shan; Ruan, Jishou; Zhang, Tao: Prediction of the parallel/antiparallel orientation of beta-strands using amino acid pairing preferences and support vector machines (2010)
  6. Bernardes, Juliana S.; Davila, Alberto Mr; Costa, Vitor S.; Zaverucha, Gerson: Improving model construction of profile hmms for remote homology detection through structural alignment (2007) ioport
  7. Burke, David F.; Worth, Catherine L.; Priego, Eva-Maria; Cheng, Tammy; Smink, Luc J.; Todd, John A.; Blundell, Tom L.: Genome bioinformatic analysis of nonsynonymous SNPs (2007) ioport
  8. Kaján, László; Rychlewski, Leszek: Evaluation of 3D-jury on CASP7 models (2007) ioport
  9. Taguchi, Y-H; Gromiha, M. Michael: Application of amino acid occurrence for discriminating different folding types of globular proteins (2007) ioport