Striped sheets and protein contact prediction

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  author =       "Robert M. MacCallum",
  title =        "Striped sheets and protein contact prediction",
  journal =      "Bioinformatics",
  year =         "2004",
  volume =       "20",
  number =       "Suppl 1",
  pages =        "I224--I231",
  month =        aug # " 4",
  keywords =     "genetic algorithms, genetic programming, SOM",
  ISSN =         "1460-2059",
  URL =          "",
  DOI =          "doi:10.1093/bioinformatics/bth913",
  size =         "8 pages",
  abstract =     "MOTIVATION: Current approaches to contact map
                 prediction in proteins have focused on amino acid
                 conservation and patterns of mutation at sequentially
                 distant positions. This sequence information is poorly
                 understood and very little progress has been made in
                 this area during recent years. RESULTS: In this study,
                 an observation of 'striped' sequence patterns across
                 beta-sheets prompted the development of a new type of
                 contact map predictor. Computer program code was
                 evolved with an evolutionary algorithm (genetic
                 programming) to select residues and residue pairs
                 likely to make contacts based solely on local sequence
                 patterns extracted with the help of self-organising
                 maps. The mean prediction accuracy is 27percent on a
                 validation set of 156 domains up to 400 residues in
                 length, where contacts are separated by at least 8
                 residues and length/10 pairs are predicted. The
                 retrospective accuracy on a set of 15 CASP5 targets is
                 27percent and 14percent for length/10 and length/2
                 predicted pairs, respectively (both using a minimum
                 residue separation of 24). This compares favourably to
                 the equivalent 21percent and 13percent obtained for the
                 best automated contact prediction methods at CASP5. The
                 results suggest that protein architectures impose
                 regularities in local sequence environments. Other
                 sources of information, such as correlated/compensatory
                 mutations, may further improve accuracy. AVAILABILITY:
                 A web-based prediction service is available at
  notes =        "PMID: 15262803 [PubMed - in process]

                 cited by \cite{Latek:2008:BMCsb}",

Genetic Programming entries for Robert M MacCallum