A large-scale evaluation of computational protein function prediction
Predrag Radivojac, Wyatt T Clark, Tal Ronnen Oron, Alexandra M Schnoes, Tobias Wittkop, Artem Sokolov, Kiley Graim, Christopher Funk, Karin Verspoor, Asa Ben-Hur, Gaurav Pandey, Jeffrey M Yunes, Ameet S Talwalkar, Susanna Repo, Michael L Souza, Damiano Piovesan, Rita Casadio, Zheng Wang, Jianlin Cheng, Hai Fang, Julian Gough, Patrik Koskinen, Petri Törönen, Jussi Nokso-Koivisto, Liisa Holm et al.
Affiliations Contributions Corresponding authors
Nature Methods 10, 221–227 (2013) doi:10.1038/nmeth.2340
Received 02 April 2012 Accepted 10 December 2012 Published online 27 January 2013
Abstract
Automated annotation of protein function is challenging. As the number of sequenced genomes rapidly grows, the overwhelming majority of protein products can only be annotated computationally. If computational predictions are to be relied upon, it is crucial that the accuracy of these methods be high. Here we report the results from the first large-scale community-based critical assessment of protein function annotation (CAFA) experiment. Fifty-four methods representing the state of the art for protein function prediction were evaluated on a target set of 866 proteins from 11 organisms. Two findings stand out: (i) today's best protein function prediction algorithms substantially outperform widely used first-generation methods, with large gains on all types of targets; and (ii) although the top methods perform well enough to guide experiments, there is considerable need for improvement of currently available tools.
Subject terms: Bioinformatics Biochemistry
