KAUST Grant NumberKUK-I1–012-43
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AbstractWe present the results of the assessment of the intramolecular residue-residue contact predictions from 26 prediction groups participating in the 10th round of the CASP experiment. The most recently developed direct coupling analysis methods did not take part in the experiment likely because they require a very deep sequence alignment not available for any of the 114 CASP10 targets. The performance of contact prediction methods was evaluated with the measures used in previous CASPs (i.e., prediction accuracy and the difference between the distribution of the predicted contacts and that of all pairs of residues in the target protein), as well as new measures, such as the Matthews correlation coefficient, the area under the precision-recall curve and the ranks of the first correctly and incorrectly predicted contact. We also evaluated the ability to detect interdomain contacts and tested whether the difficulty of predicting contacts depends upon the protein length and the depth of the family sequence alignment. The analyses were carried out on the target domains for which structural homologs did not exist or were difficult to identify. The evaluation was performed for all types of contacts (short, medium, and long-range), with emphasis placed on long-range contacts, i.e. those involving residues separated by at least 24 residues along the sequence. The assessment suggests that the best CASP10 contact prediction methods perform at approximately the same level, and comparably to those participating in CASP9.
CitationMonastyrskyy B, D’Andrea D, Fidelis K, Tramontano A, Kryshtafovych A (2013) Evaluation of residue-residue contact prediction in CASP10. Proteins: Structure, Function, and Bioinformatics 82: 138–153. Available: http://dx.doi.org/10.1002/prot.24340.
SponsorsGrant sponsor: US National Institute of General Medical Sciences (NIGMS/NIH); Grant number: R01GM100482 (to K.F.); Grant sponsor: KAUST Award; Grant number: KUK-I1–012-43 (to A.T.); Grant sponsor: EMBO.
PubMed Central IDPMC3823628
CollectionsPublications Acknowledging KAUST Support
- Evaluation of residue-residue contact predictions in CASP9.
- Authors: Monastyrskyy B, Fidelis K, Tramontano A, Kryshtafovych A
- Issue date: 2011
- Assessment of protein disorder region predictions in CASP10.
- Authors: Monastyrskyy B, Kryshtafovych A, Moult J, Tramontano A, Fidelis K
- Issue date: 2014 Feb
- Improving accuracy of protein contact prediction using balanced network deconvolution.
- Authors: Sun HP, Huang Y, Wang XF, Zhang Y, Shen HB
- Issue date: 2015 Mar
- A study and benchmark of DNcon: a method for protein residue-residue contact prediction using deep networks.
- Authors: Eickholt J, Cheng J
- Issue date: 2013
- New encouraging developments in contact prediction: Assessment of the CASP11 results.
- Authors: Monastyrskyy B, D'Andrea D, Fidelis K, Tramontano A, Kryshtafovych A
- Issue date: 2016 Sep