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Proteins Structure Function and Bioinformatics
Article . 2013 . Peer-reviewed
License: Wiley Online Library User Agreement
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Evaluation of residue–residue contact prediction in CASP10

Authors: B. Monastyrskyy; D. D’Andrea; K. Fidelis; TRAMONTANO, ANNA; A. Kryshtafovych;

Evaluation of residue–residue contact prediction in CASP10

Abstract

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. Proteins 2014; 82(Suppl 2):138–153. © 2013 Wiley Periodicals, Inc.

Countries
Italy, United Kingdom, Saudi Arabia
Keywords

Models, Molecular, Protein Folding, Models, Statistical, Protein Conformation, Molecular, Computational Biology, Proteins, Statistical, RR, Residue-residue Contact Prediction, Models, Sequence Analysis, Protein, Casp, Computer Simulation, Algorithms

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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
76
Top 10%
Top 10%
Top 1%
bronze