University of CaliforniaDavis 95616California

University of CaliforniaDavis 95616California


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Monastyrskyy B.,University of CaliforniaDavis 95616California | Fidelis K.,University of CaliforniaDavis 95616California | Kryshtafovych A.,University of CaliforniaDavis 95616California
Proteins: Structure, Function and Bioinformatics | Year: 2015

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). © 2015 Wiley Periodicals, Inc.


Kryshtafovych A.,University of CaliforniaDavis 95616California | Moult J.,University of MarylandRockville 20850Maryland | Basle A.,Institute for Cell and Molecular Biosciences | Burgin A.,Broad InstituteCambridge 02142Massachusetts | And 8 more authors.
Proteins: Structure, Function and Bioinformatics | Year: 2015

The Critical Assessment of protein Structure Prediction (CASP) experiment would not have been possible without the prediction targets provided by the experimental structural biology community. In this article, selected crystallographers providing targets for the CASP11 experiment discuss the functional and biological significance of the target proteins, highlight their most interesting structural features, and assess whether these features were correctly reproduced in the predictions submitted to CASP11. © 2015 The Authors. Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc.

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