title: New encouraging developments in contact prediction: Assessment of the CASP11 results.
abstract: This article provides a report on the state-of-the-art in the prediction of intra-molecular residue-residue contacts in proteins based on the assessment of the predictions submitted to the CASP11 experiment. The assessment emphasis is placed on the accuracy in predicting long-range contacts. Twenty-nine groups participated in contact prediction in CASP11. At least eight of them used the recently developed evolutionary coupling techniques, with the top group (CONSIP2) reaching precision of 27% on target proteins that could not be modeled by homology. This result indicates a breakthrough in the development of methods based on the correlated mutation approach. Successful prediction of contacts was shown to be practically helpful in modeling three-dimensional structures; in particular target T0806 was modeled exceedingly well with accuracy not yet seen for ab initio targets of this size (>250 residues). Proteins 2016; 84(Suppl 1):131-144. © 2015 Wiley Periodicals, Inc.
authors.affiliation: Genome Center, University of California, Davis, California, 95616.
authors.forename: Bohdan
authors.initials: B
authors.lastname: Monastyrskyy
authors.affiliation: Department of Physics, Sapienza-University of Rome, Rome, 00185, Italy.
authors.forename: Daniel
authors.initials: D
authors.lastname: D'Andrea
authors.affiliation: Genome Center, University of California, Davis, California, 95616.
authors.forename: Krzysztof
authors.initials: K
authors.lastname: Fidelis
authors.affiliation: Department of Physics, Sapienza-University of Rome, Rome, 00185, Italy.|Istituto Pasteur-Fondazione Cenci Bolognetti-University of Rome, Rome, 00185, Italy.
authors.forename: Anna
authors.initials: A
authors.lastname: Tramontano
authors.affiliation: Genome Center, University of California, Davis, California, 95616. akryshtafovych@ucdavis.edu.
authors.forename: Andriy
authors.initials: A
authors.lastname: Kryshtafovych
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D001419:Bacteria / Q000737:chemistry; D019295:Computational Biology / Q000379:methods / Q000706:statistics & numerical data*; D003198:Computer Simulation; D030562:Databases, Protein; D029968:Escherichia coli Proteins / Q000737:chemistry*; D006801:Humans; D007391:International Cooperation; D020407:Internet; D008958:Models, Molecular; D015233:Models, Statistical; D017510:Protein Folding; D054730:Protein Interaction Domains and Motifs; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D016415:Sequence Alignment; D012984:Software
chemical_list: D029968:Escherichia coli Proteins; D011506:Proteins; C559319:YaaA protein, E coli
keywords: CASP; co-variation; contact prediction; correlated mutations; evolutionary coupling