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; Domenico Cozzetto; Daniel W A Buchan; Kevin Bryson; David T Jones; Bhakti Limaye; 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 Böhm; Tatjana Braun; Maximilian Hecht; Mark Heron; Peter Hönigschmid; Thomas 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; Amos Bairoch; Michal Linial; Patricia C Babbitt; Steven E Brenner; Christine Orengo; Burkhard Rost; Sean D Mooney; Iddo Friedberg

doi:10.1038/nmeth.2340

Back

A large-scale evaluation of computational protein function prediction

Journal article

Open access

Peer reviewed

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, …

Nature methods, Vol.10(3), pp.221-227

2013-03

DOI: https://doi.org/10.1038/nmeth.2340

PMCID: PMC3584181

PMID: 23353650

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 eleven organisms. Two findings stand out: (i) today’s best protein function prediction algorithms significantly outperformed 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 significant need for improvement of currently available tools.

Files and links (1)

url

https://doi.org/10.1038/nmeth.2340View

Published (Version of record) Open

Metrics

4 Record Views

613 Times Cited - Web of Science

See more details

InCites Highlights

These are selected metrics from InCites Benchmarking & Analytics tool, related to this output

Highly Cited Paper

Collaboration types: Industry collaboration; Domestic collaboration; International collaboration
Citation topics: 1 Clinical & Life Sciences; 1.54 Molecular & Cell Biology - Genetics; 1.54.79 Gene Expression Data
Web Of Science research areas: Biochemical Research Methods
ESI research areas: Biology & Biochemistry

UN Sustainable Development Goals (SDGs)

This output has contributed to the advancement of the following goals:

Source: InCites

Details

Title: A large-scale evaluation of computational protein function prediction
Creators: Predrag Radivojac - School of Informatics and Computing, Indiana University, Bloomington, Indiana, USA
Wyatt T Clark - School of Informatics and Computing, Indiana University, Bloomington, Indiana, USA
Tal Ronnen Oron - Buck Institute for Research on Aging, Novato, California, USA
Alexandra M Schnoes - Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California, USA
Tobias Wittkop - Buck Institute for Research on Aging, Novato, California, USA
Artem Sokolov - Department of Computer Science, Colorado State University, Fort Collins, Colorado, USA
Kiley Graim - Department of Computer Science, Colorado State University, Fort Collins, Colorado, USA
Christopher Funk - Computational Bioscience Program, University of Colorado School of Medicine, Aurora, Colorado, USA
Karin Verspoor - Computational Bioscience Program, University of Colorado School of Medicine, Aurora, Colorado, USA
Asa Ben-Hur - Department of Computer Science, Colorado State University, Fort Collins, Colorado, USA
Gaurav Pandey - Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
Jeffrey M Yunes - Joint Graduate Group in Bioengineering, University of California, Berkeley, California, USA
Ameet S Talwalkar - Department of Electrical Engineering and Computer Science, University of California, Berkeley, California, USA
Susanna Repo - Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
Michael L Souza - Biophysics Graduate Program, University of California, Berkeley, California, USA
Damiano Piovesan - Department of Biology, University of Bologna, Bologna, Italy
Rita Casadio - Department of Biology, University of Bologna, Bologna, Italy
Zheng Wang - Department of Computer Science, University of Missouri, Columbia, Missouri, USA
Jianlin Cheng - Department of Computer Science, University of Missouri, Columbia, Missouri, USA
Hai Fang - Department of Computer Science, University of Bristol, Bristol, UK
Julian Gough - Department of Computer Science, University of Bristol, Bristol, UK
Patrik Koskinen - Department of Biological and Environmental Sciences, Viikki Biocentre, University of Helsinki, Helsinki, Finland
Petri Törönen - Department of Biological and Environmental Sciences, Viikki Biocentre, University of Helsinki, Helsinki, Finland
Jussi Nokso-Koivisto - Department of Biological and Environmental Sciences, Viikki Biocentre, University of Helsinki, Helsinki, Finland
Liisa Holm - Department of Biological and Environmental Sciences, Viikki Biocentre, University of Helsinki, Helsinki, Finland
Domenico Cozzetto - Department of Computer Science, University College London, London, UK
Daniel W A Buchan - Department of Computer Science, University College London, London, UK
Kevin Bryson - Department of Computer Science, University College London, London, UK
David T Jones - Department of Computer Science, University College London, London, UK
Bhakti Limaye - Bioinformatics Group, Centre for Development of Advanced Computing, Pune University Campus, Pune, India
Harshal Inamdar - Bioinformatics Group, Centre for Development of Advanced Computing, Pune University Campus, Pune, India
Avik Datta - Bioinformatics Group, Centre for Development of Advanced Computing, Pune University Campus, Pune, India
Sunitha K Manjari - Bioinformatics Group, Centre for Development of Advanced Computing, Pune University Campus, Pune, India
Rajendra Joshi - Bioinformatics Group, Centre for Development of Advanced Computing, Pune University Campus, Pune, India
Meghana Chitale - Department of Computer Science, Purdue University, West Lafayette, Indiana, USA
Daisuke Kihara - Department of Computer Science, Purdue University, West Lafayette, Indiana, USA
Andreas M Lisewski - Department of Molecular and Human Genetics, Computational and Integrative Biomedical Research Center, Baylor College of Medicine, Houston, Texas, USA
Serkan Erdin - Department of Molecular and Human Genetics, Computational and Integrative Biomedical Research Center, Baylor College of Medicine, Houston, Texas, USA
Eric Venner - Department of Molecular and Human Genetics, Computational and Integrative Biomedical Research Center, Baylor College of Medicine, Houston, Texas, USA
Olivier Lichtarge - Department of Molecular and Human Genetics, Computational and Integrative Biomedical Research Center, Baylor College of Medicine, Houston, Texas, USA
Robert Rentzsch - University College London, Institute for Structural and Molecular Biology, London, UK
Haixuan Yang - Department of Computer Science, Centre for Systems and Synthetic Biology, Royal Holloway, University of London, Egham, UK
Alfonso E Romero - Department of Computer Science, Centre for Systems and Synthetic Biology, Royal Holloway, University of London, Egham, UK
Prajwal Bhat - Department of Computer Science, Centre for Systems and Synthetic Biology, Royal Holloway, University of London, Egham, UK
Alberto Paccanaro - Department of Computer Science, Centre for Systems and Synthetic Biology, Royal Holloway, University of London, Egham, UK
Tobias Hamp - Technische Universität München, Bioinformatik - i12, Informatik, Garching, Germany
Rebecca Kassner - Technische Universität München, Bioinformatik - i12, Informatik, Garching, Germany
Stefan Seemayer - Technische Universität München, Bioinformatik - i12, Informatik, Garching, Germany
Esmeralda Vicedo - Technische Universität München, Bioinformatik - i12, Informatik, Garching, Germany
Christian Schaefer - Technische Universität München, Bioinformatik - i12, Informatik, Garching, Germany
Dominik Achten - Technische Universität München, Bioinformatik - i12, Informatik, Garching, Germany
Florian Auer - Technische Universität München, Bioinformatik - i12, Informatik, Garching, Germany
Ariane Böhm - Technische Universität München, Bioinformatik - i12, Informatik, Garching, Germany
Tatjana Braun - Technische Universität München, Bioinformatik - i12, Informatik, Garching, Germany
Maximilian Hecht - Technische Universität München, Bioinformatik - i12, Informatik, Garching, Germany
Mark Heron - Technische Universität München, Bioinformatik - i12, Informatik, Garching, Germany
Peter Hönigschmid - Technische Universität München, Bioinformatik - i12, Informatik, Garching, Germany
Thomas Hopf - Technische Universität München, Bioinformatik - i12, Informatik, Garching, Germany
Stefanie Kaufmann - Technische Universität München, Bioinformatik - i12, Informatik, Garching, Germany
Michael Kiening - Technische Universität München, Bioinformatik - i12, Informatik, Garching, Germany
Denis Krompass - Technische Universität München, Bioinformatik - i12, Informatik, Garching, Germany
Cedric Landerer - Technische Universität München, Bioinformatik - i12, Informatik, Garching, Germany
Yannick Mahlich - Technische Universität München, Bioinformatik - i12, Informatik, Garching, Germany
Manfred Roos - Technische Universität München, Bioinformatik - i12, Informatik, Garching, Germany
Jari Björne - Department of Information Technology, University of Turku, Turku Centre for Computer Science, Turku, Finland
Tapio Salakoski - Department of Information Technology, University of Turku, Turku Centre for Computer Science, Turku, Finland
Andrew Wong - School of Computing, Queen’s University, Kingston, Ontario, Canada
Hagit Shatkay - School of Computing, Queen’s University, Kingston, Ontario, Canada
Fanny Gatzmann - Max-Planck-Institute for Informatics, Saarbrücken, Germany
Ingolf Sommer - Max-Planck-Institute for Informatics, Saarbrücken, Germany
Mark N Wass - Centre for Bioinformatics, Division of Molecular Biosciences, Imperial College, London, UK
Michael J E Sternberg - Centre for Bioinformatics, Division of Molecular Biosciences, Imperial College, London, UK
Nives Škunca - Division of Electronics, Ruder Boškovic Institute, Zagreb, Croatia
Fran Supek - Division of Electronics, Ruder Boškovic Institute, Zagreb, Croatia
Matko Bošnjak - Division of Electronics, Ruder Boškovic Institute, Zagreb, Croatia
Panče Panov - Department of Knowledge Technologies, Jožef Stefan Institute, Ljubljana, Slovenia
Sašo Džeroski - Department of Knowledge Technologies, Jožef Stefan Institute, Ljubljana, Slovenia
Tomislav Šmuc - Division of Electronics, Ruder Boškovic Institute, Zagreb, Croatia
Yiannis A I Kourmpetis - Biometris, Wageningen University and Research Centre, Wageningen, The Netherlands
Aalt D J van Dijk - Applied Bioinformatics, Plant Research International, Wageningen, The Netherlands
Cajo J F ter Braak - Biometris, Wageningen University and Research Centre, Wageningen, The Netherlands
Yuanpeng Zhou - Institute of Biostatistics, School of Life Sciences, Fudan University, Shanghai, China
Qingtian Gong - Institute of Biostatistics, School of Life Sciences, Fudan University, Shanghai, China
Xinran Dong - Institute of Biostatistics, School of Life Sciences, Fudan University, Shanghai, China
Weidong Tian - Institute of Biostatistics, School of Life Sciences, Fudan University, Shanghai, China
Marco Falda - Department of Molecular Medicine, University of Padova, Padova, Italy
Paolo Fontana - Istituto Agrario San Michele all’Adige Research and Innovation Centre, Trento, Italy
Enrico Lavezzo - Department of Molecular Medicine, University of Padova, Padova, Italy
Barbara Di Camillo - Department of Information Engineering, University of Padova, Padova, Italy
Stefano Toppo - Department of Molecular Medicine, University of Padova, Padova, Italy
Liang Lan - Department of Computer and Information Sciences, Temple University, Philadelphia, Pennsylvania, USA
Nemanja Djuric - Department of Computer and Information Sciences, Temple University, Philadelphia, Pennsylvania, USA
Yuhong Guo - Department of Computer and Information Sciences, Temple University, Philadelphia, Pennsylvania, USA
Slobodan Vucetic - Department of Computer and Information Sciences, Temple University, Philadelphia, Pennsylvania, USA
Amos Bairoch - Swiss Institute of Bioinformatics, Geneva, Switzerland and Department of Human Protein Sciences, University of Geneva, Geneva, Switzerland
Michal Linial - Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Israel
Patricia C Babbitt - Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California, USA
Steven E Brenner - Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
Christine Orengo - University College London, Institute for Structural and Molecular Biology, London, UK
Burkhard Rost - Technische Universität München, Bioinformatik - i12, Informatik, Garching, Germany
Sean D Mooney - Buck Institute for Research on Aging, Novato, California, USA
Iddo Friedberg - Department of Microbiology, Miami University, Oxford, Ohio, USA
Publication Details: Nature methods, Vol.10(3), pp.221-227
Academic Unit: College of A&S; A&S - Computer Science
Language: English
Resource Type: Journal article
PMID: 23353650
PMCID: PMC3584181
Record Identifier: 991031599087402976