title: Protein topology from predicted residue contacts.
abstract: Residue contacts predicted from correlated positions in a multiple sequence alignment are often sparse and uncertain. To some extent, these limitations in the data can be overcome by grouping the contacts by secondary structure elements and enumerating the possible packing arrangements of these elements in a combinatorial manner. Strong interactions appear frequently but inconsistent interactions are down-weighted and missing interactions up-weighted. The resulting improved consistency in the predicted interactions has allowed the method to be successfully applied to proteins up to 200 residues in length which is larger than any structure previously predicted using sequence data alone.
authors.affiliation: Division of Mathematical Biology, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London, United Kingdom. wtaylor@nimr.mrc.ac.uk
authors.forename: William R
authors.initials: WR
authors.lastname: Taylor
authors.forename: David T
authors.initials: DT
authors.lastname: Jones
authors.forename: Michael I
authors.initials: MI
authors.lastname: Sadowski
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D019295:Computational Biology / Q000379:methods; D008954:Models, Biological; D008958:Models, Molecular; D015233:Models, Statistical; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D011485:Protein Binding / Q000235:genetics / Q000502:physiology; D011487:Protein Conformation; D017510:Protein Folding; D054730:Protein Interaction Domains and Motifs / Q000235:genetics / Q000502:physiology*; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid
chemical_list: D011506:Proteins
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