title: Sequence-structure homology recognition by iterative alignment refinement and comparative modeling.
abstract: Our approach to fold recognition for the fourth critical assessment of techniques for protein structure prediction (CASP4) experiment involved the use of the FUGUE sequence-structure homology recognition program (http://www-cryst.bioc.cam.ac.uk/fugue), followed by model building. We treat models as hypotheses and examine these to determine whether they explain the available data. Our method depends heavily on environment-specific substitution tables derived from our database of structural alignments of homologous proteins (HOMSTRAD, http://www-cryst.bioc.cam.ac.uk/homstrad/). FUGUE uses these tables to incorporate structural information into profiles created from HOMSTRAD alignments that are matched against a profile created for the target from multiple sequence alignment. In addition, environment-specific substitution tables are used throughout the modeling procedure and as part of the model evaluation. Annotation of sequence alignments with JOY, to reflect local structural features, proved valuable, both for modifying hypotheses, and for rejecting predictions when the expected pattern of conservation is not observed. Our stringency in rejecting incorrect predictions led us to submit a relatively small number of models, including only a low number of false positives, resulting in a high average score.
authors.affiliation: Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom.
authors.forename: M G
authors.initials: MG
authors.lastname: Williams
authors.forename: H
authors.initials: H
authors.lastname: Shirai
authors.forename: J
authors.initials: J
authors.lastname: Shi
authors.forename: H G
authors.initials: HG
authors.lastname: Nagendra
authors.forename: J
authors.initials: J
authors.lastname: Mueller
authors.forename: K
authors.initials: K
authors.lastname: Mizuguchi
authors.forename: R N
authors.initials: RN
authors.lastname: Miguel
authors.forename: S C
authors.initials: SC
authors.lastname: Lovell
authors.forename: C A
authors.initials: CA
authors.lastname: Innis
authors.forename: C M
authors.initials: CM
authors.lastname: Deane
authors.forename: L
authors.initials: L
authors.lastname: Chen
authors.forename: N
authors.initials: N
authors.lastname: Campillo
authors.forename: D F
authors.initials: DF
authors.lastname: Burke
authors.forename: T L
authors.initials: TL
authors.lastname: Blundell
authors.forename: P I
authors.initials: PI
authors.lastname: de Bakker
mesh_terms: D000595:Amino Acid Sequence; D050260:Carbohydrate Metabolism; D002265:Carboxylic Ester Hydrolases / Q000737:chemistry; D003198:Computer Simulation; D003598:Cytoskeletal Proteins / Q000737:chemistry; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011133:Polysaccharide-Lyases / Q000737:chemistry; D011485:Protein Binding; D017510:Protein Folding; D017434:Protein Structure, Tertiary; D020539:Sequence Analysis, Protein; D017386:Sequence Homology, Amino Acid; D012984:Software; D051178:alpha Catenin
chemical_list: D003598:Cytoskeletal Proteins; D051178:alpha Catenin; D002265:Carboxylic Ester Hydrolases; C022323:pectinesterase; D011133:Polysaccharide-Lyases; C023911:pectate lyase