Evaluation of residue-residue contact prediction in CASP10.

Abstract : We 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.
Type de document :
Article dans une revue
Proteins - Structure, Function and Bioinformatics, Wiley, 2014, 82 Suppl 2, pp.138-53. 〈10.1002/prot.24340〉
Liste complète des métadonnées

Littérature citée [44 références]  Voir  Masquer  Télécharger

https://hal-riip.archives-ouvertes.fr/pasteur-01202597
Contributeur : Istituto Pasteur Fondazione Cenci Bolognetti <>
Soumis le : lundi 21 septembre 2015 - 13:57:01
Dernière modification le : vendredi 23 février 2018 - 08:46:02
Document(s) archivé(s) le : mardi 29 décembre 2015 - 08:58:15

Fichier

nihms492315.pdf
Fichiers produits par l'(les) auteur(s)

Licence


Distributed under a Creative Commons Paternité - Pas d'utilisation commerciale - Pas de modification 4.0 International License

Identifiants

Collections

Citation

Bohdan Monastyrskyy, Daniel D'Andrea, Krzysztof Fidelis, Anna Tramontano, Andriy Kryshtafovych. Evaluation of residue-residue contact prediction in CASP10.. Proteins - Structure, Function and Bioinformatics, Wiley, 2014, 82 Suppl 2, pp.138-53. 〈10.1002/prot.24340〉. 〈pasteur-01202597〉

Partager

Métriques

Consultations de la notice

163

Téléchargements de fichiers

71