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A Large-Scale Evaluation of Computational Protein Function Prediction

Predrag Radivojac, Wyatt T. Clark, Tal Ronnen Oron, Alexandra M. Schnoes, Tobias Wittkop 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, Domenico Cozzetto, Daniel W. A. Buchan, Kevin Bryson, David T. Jones, Bhakt Limave, Harshal Inamdar, Avik Datta, Sunitha K. Manjari, Rajendra Joshi, Meghana Chitale, Daisuke Kihara, Andreas M. Lisewski, Serkan Erdin, Eric Venner, Olivier Lichtarge, Robert Rentzsch, Haixuan Yang, Alfonso E. Romero, Prajwal Bhat, Alberto Paccanaro, Tobias Hamp, Rebecca Kaßner, Stefan Seemayer, Esmeralda Vicedo, Christian Schaefer, Dominik Achten, Florian Auer, Ariane Boehm, Tatjana Braun, Maximilian Hecht, Mark Heron, Peter Hönigschmid, Thomas A. Hopf, Stefanie Kaufmann, Michael Kiening, Denis Krompass, Cedric Landerer, Yannick Mahlich, Manfred Roos, Jari Björne, Tapio Salakoski, Andrew Wong, Hagit Shatkay, Fanny Gatzmann, Ingolf Sommer, Mark N. Wass, Michael J. E. Sternberg, Nives Škunca, Fran Supek, Matko Bošnjak, Panče Panov, Sašo Džeroski, Tomislav Šmuc, Yiannis A. I. Kourmpetis, Aalt D. J. van Dijk, Cajo J. F. ter Braak, Yuanpeng Zhou, Qingtian Gong, Xinran Dong, Weidong Tian, Marco Falda, Paolo Fontana, Enrico Lavezzo, Barbara Di Camillo, Stefano Toppo, Liang Lan, Nemanja Djuric, Yuhong Guo, Slobodan Vucetic Vucetic, Amos Bairoch, Michal Linial, Patricia C. Babbitt, Steven E. Brenner, Christine Orengo, Burkhard Rost, Sean D. Mooney, Iddo Friedberg, A Large-Scale Evaluation of Computational Protein Function Prediction. Nature methods 10, 221–227, 2013.


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.

BibTeX entry:

  title = {A Large-Scale Evaluation of Computational Protein Function Prediction},
  author = {Radivojac, Predrag and Clark, Wyatt T. and Oron, Tal Ronnen and Schnoes, Alexandra M. and Wittkop, Tobias Wittkop and Sokolov, Artem and Graim, Kiley and Funk, Christopher and Verspoor, Karin and Ben-Hur, Asa and Pandey, Gaurav and Yunes, Jeffrey M. and Talwalkar, Ameet S. and Repo, Susanna and Souza, Michael L. and Piovesan, Damiano and Casadio, Rita and Wang, Zheng and Cheng, Jianlin and Fang, Hai and Gough, Julian and Koskinen, Patrik and Törönen, Petri and Nokso-Koivisto, Jussi and Holm, Liisa and Cozzetto, Domenico and Buchan, Daniel W. A. and Bryson, Kevin and Jones, David T. and Limave, Bhakt and Inamdar, Harshal and Datta, Avik and Manjari, Sunitha K. and Joshi, Rajendra and Chitale, Meghana and Kihara, Daisuke and Lisewski, Andreas M. and Erdin, Serkan and Venner, Eric and Lichtarge, Olivier and Rentzsch, Robert and Yang, Haixuan and Romero, Alfonso E. and Bhat, Prajwal and Paccanaro, Alberto and Hamp, Tobias and Kaßner, Rebecca and Seemayer, Stefan and Vicedo, Esmeralda and Schaefer, Christian and Achten, Dominik and Auer, Florian and Boehm, Ariane and Braun, Tatjana and Hecht, Maximilian and Heron, Mark and Hönigschmid, Peter and Hopf, Thomas A. and Kaufmann, Stefanie and Kiening, Michael and Krompass, Denis and Landerer, Cedric and Mahlich, Yannick and Roos, Manfred and Björne, Jari and Salakoski, Tapio and Wong, Andrew and Shatkay, Hagit and Gatzmann, Fanny and Sommer, Ingolf and Wass, Mark N. and Sternberg, Michael J. E. and Škunca, Nives and Supek, Fran and Bošnjak, Matko and Panov, Panče and Džeroski, Sašo and Šmuc, Tomislav and Kourmpetis, Yiannis A. I. and Dijk, Aalt D. J. van and Braak, Cajo J. F. ter and Zhou, Yuanpeng and Gong, Qingtian and Dong, Xinran and Tian, Weidong and Falda, Marco and Fontana, Paolo and Lavezzo, Enrico and Camillo, Barbara Di and Toppo, Stefano and Lan, Liang and Djuric, Nemanja and Guo, Yuhong and Vucetic, Slobodan Vucetic and Bairoch, Amos and Linial, Michal and Babbitt, Patricia C. and Brenner, Steven E. and Orengo, Christine and Rost, Burkhard and Mooney, Sean D. and Friedberg, Iddo},
  journal = {Nature methods},
  volume = {10},
  publisher = {Nature Publishing Group},
  pages = {221–227},
  year = {2013},

Belongs to TUCS Research Unit(s): Turku BioNLP Group

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