Contact prediction in protein modeling: Scoring, folding and refinement of coarse-grained models

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@Article{Latek:2008:BMCsb,
  author =       "Dorota Latek and Andrzej Kolinski",
  title =        "Contact prediction in protein modeling: Scoring,
                 folding and refinement of coarse-grained models",
  journal =      "BMC Structural Biology",
  year =         "2008",
  volume =       "8",
  number =       "36",
  month =        aug # " 11",
  keywords =     "genetic algorithms, genetic programming",
  DOI =          "doi:10.1186/1472-6807-8-36",
  abstract =     "Several different methods for contact prediction
                 succeeded within the Sixth Critical Assessment of
                 Techniques for Protein Structure Prediction (CASP6).
                 The most relevant were non-local contact predictions
                 for targets from the most difficult categories: fold
                 recognition-analogy and new fold. Such contacts could
                 provide valuable structural information in case a
                 template structure cannot be found in the
                 PDB.

                 Results

                 We described comprehensive tests of the effectiveness
                 of contact data in various aspects of de novo modeling
                 with CABS, an algorithm which was used successfully in
                 CASP6 by the Kolinski-Bujnicki group. We used the
                 predicted contacts in a simple scoring function for the
                 post-simulation ranking of protein models and as a soft
                 bias in the folding simulations and in the
                 fold-refinement procedure. The latter approach turned
                 out to be the most successful. The CABS force field
                 used in the Replica Exchange Monte Carlo simulations
                 cooperated with the true contacts and discriminated the
                 false ones, which resulted in an improvement of the
                 majority of Kolinski-Bujnicki's protein models. In the
                 modeling we tested different sets of predicted contact
                 data submitted to the CASP6 server. According to our
                 results, the best performing were the contacts with the
                 accuracy balanced with the coverage, obtained either
                 from the best two predictors only or by a consensus
                 from as many predictors as possible.

                 Conclusion

                 Our tests have shown that theoretically predicted
                 contacts can be very beneficial for protein structure
                 prediction. Depending on the protein modeling method, a
                 contact data set applied should be prepared with
                 differently balanced coverage and accuracy of predicted
                 contacts. Namely, high coverage of contact data is
                 important for the model ranking and high accuracy for
                 the folding simulations.",
  notes =        "PMID:",
}

Genetic Programming entries for Dorota Latek Andrzej Kolinski

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