PSICQUIC and PSISCORE: accessing and scoring molecular interactions (original) (raw)

To the Editor:

To study proteins in the context of a cellular system, it is essential that the molecules with which a protein interacts are identified and the functional consequence of each interaction is understood. A plethora of resources now exist to capture molecular interaction data from the many laboratories generating such information, but whereas such databases are rich in information, the sheer number and variability of such databases constitutes a substantial challenge in both data access and quality assessment to the researchers interested in a specific biological domain.

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Acknowledgements

This study was supported by the European Commission under the Serving Life-science Information for the Next Generation contract 226073; Proteomics Standards Initiative and International Molecular Exchange contract FP7-HEALTH-2007-223411; Apoptosis Systems Biology Applied to Cancer and AIDS contract FP7-HEALTH-2007-200767; Experimental Network for Functional Integration contract LSHG-CT-2005-518254; German National Genome Research Network; German Research Foundation contract KFO 129/1-2; US National Institutes of Health grant R01GM071909; the Italian Association for Cancer Research; a Wellcome Trust Strategic Award to the European Molecular Biology Laboratory–European Bioinformatics Institute for Chemogenomics Databases; Grand Challenges in Global Health Research, the Canadian Institutes of Health Research, Foundation for the National Institutes of Health and Genome British Columbia; and a German Research Foundation–funded Cluster of Excellence for Multimodal Computing and Interaction. We thank organizers and sponsors of the Biohackathons 2008, 2009 and 2010 where part of the work was done.

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Author notes

1. Bruno Aranda and Hagen Blankenburg: These authors contributed equally to this work.

Authors and Affiliations

1. European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
   Bruno Aranda, Samuel Kerrien, Jose M Dana, Marine Dumousseau, Anna Gaulton, Rafael C Jimenez, Jyoti Khadake, Gavin O'Kelly, Sandra Orchard, Sameer Velankar, Gerard J Kleywegt, John Overington & Henning Hermjakob
2. Max Planck Institute for Informatics, Saarbrücken, Germany
   Hagen Blankenburg & Mario Albrecht
3. Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
   Fiona S L Brinkman
4. Institute for Research in Biomedicine, Barcelona, Spain
   Arnaud Ceol
5. Department of Biology, University of Rome Tor Vergata, Rome, Italy
   Arnaud Ceol, Eugenia Galeota & Gianni Cesareni
6. Institut de Biologie et Chimie des Protéines, Unité Mixte de Recherche 5086, Centre National de la Recherche Scientifique–Université Lyon 1, Lyon, France
   Emilie Chautard & Sylvie Ricard-Blum
7. Ontario Institute for Cancer Research, Toronto, Ontario, Canada
   Emilie Chautard & Guanming Wu
8. Cancer Research Center, Centro de Investigación de Cáncer–Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas, Universidad de Salamanca, Salamanca, Spain
   Javier De Las Rivas & Carlos Prieto
9. Istituto di Ricovero e Cura a Carattere Scientifico, Fondazione S. Lucia, Rome, Italy
   Eugenia Galeota & Gianni Cesareni
10. J. Craig Venter Institute, Rockville, Maryland, USA
    Johannes Goll
11. Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, British Columbia, Canada
    Robert E W Hancock
12. The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
    Ruth Isserlin, Magali Michaut & Gary D Bader
13. Centre for Molecular and Biomolecular Informatics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
    Jules Kerssemakers
14. Animal and Bioscience Research Department, Animal and Grassland Research Innovation Centre, Teagasc, Ireland
    David J Lynn
15. University of California, Trey Ideker Lab, San Diego, School of Medicine, La Jolla, California, USA
    Keiichiro Ono
16. Institute of Biotechnology of León, León, Spain
    Carlos Prieto
17. The Biotechnology Centre of Oslo, University of Oslo, Oslo, Norway
    Sabry Razick & Ian M Donaldson
18. Department of Informatics, Biomedical Research Group, University of Oslo, Oslo, Norway
    Sabry Razick
19. Center for Biological Sequence Analysis, BioCentrum, Technical University of Denmark, Kongens Lyngby, Denmark
    Olga Rigina
20. Department of Energy Institute for Genomics and Proteomics, University of California, Los Angeles, Los Angeles, California, USA
    Lukasz Salwinski & David Eisenberg
21. Faculty of Science, Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
    Milan Simonovic
22. Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland
    Andrew Winter & Mike Tyers
23. Department for Molecular Biosciences, University of Oslo, Oslo, Norway
    Ian M Donaldson
24. Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California, USA
    David Eisenberg
25. Howard Hughes Medical Institute, University of California, Los Angeles, California, USA
    David Eisenberg
26. Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
    Mike Tyers

Authors

1. Bruno Aranda
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2. Hagen Blankenburg
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3. Samuel Kerrien
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4. Fiona S L Brinkman
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5. Arnaud Ceol
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6. Emilie Chautard
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7. Jose M Dana
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8. Javier De Las Rivas
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9. Marine Dumousseau
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10. Eugenia Galeota
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11. Anna Gaulton
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12. Johannes Goll
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13. Robert E W Hancock
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14. Ruth Isserlin
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15. Rafael C Jimenez
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16. Jyoti Khadake
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17. David J Lynn
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18. Magali Michaut
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19. Gavin O'Kelly
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20. Keiichiro Ono
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21. Sandra Orchard
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22. Carlos Prieto
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23. Sabry Razick
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24. Olga Rigina
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25. Lukasz Salwinski
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26. Milan Simonovic
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27. Sameer Velankar
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28. Andrew Winter
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29. Guanming Wu
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30. Gary D Bader
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31. Gianni Cesareni
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32. Ian M Donaldson
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33. David Eisenberg
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34. Gerard J Kleywegt
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35. John Overington
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36. Sylvie Ricard-Blum
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37. Mike Tyers
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38. Mario Albrecht
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39. Henning Hermjakob
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Corresponding author

Correspondence toBruno Aranda.

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The authors declare no competing financial interests.

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Aranda, B., Blankenburg, H., Kerrien, S. et al. PSICQUIC and PSISCORE: accessing and scoring molecular interactions.Nat Methods 8, 528–529 (2011). https://doi.org/10.1038/nmeth.1637

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• Published: 29 June 2011
• Issue Date: July 2011
• DOI: https://doi.org/10.1038/nmeth.1637