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Proteome-wide, Structure-Based Prediction of Protein-Protein Interactions/New Molecular Interactions Viewer

Shaowei Dong, Vincent Lau, Richard Song, Matthew Ierullo, Eddi Esteban, Yingzhou Wu, Teeratham Sivieng, Hardeep Nahal, Allison Gaudinier, Asher Pasha, Rose Oughtred, Kara Dolinski, Mike Tyers, Siobhan M. Brady, Ruth Grene, Björn Usadel, Nicholas J. Provart
Shaowei Dong
aDepartment of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, 25 Willcocks St., University of Toronto, Toronto, Ontario M5S 3B2, Canada
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Vincent Lau
aDepartment of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, 25 Willcocks St., University of Toronto, Toronto, Ontario M5S 3B2, Canada
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Richard Song
aDepartment of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, 25 Willcocks St., University of Toronto, Toronto, Ontario M5S 3B2, Canada
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  • ORCID record for Richard Song
Matthew Ierullo
aDepartment of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, 25 Willcocks St., University of Toronto, Toronto, Ontario M5S 3B2, Canada
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Eddi Esteban
aDepartment of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, 25 Willcocks St., University of Toronto, Toronto, Ontario M5S 3B2, Canada
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Yingzhou Wu
aDepartment of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, 25 Willcocks St., University of Toronto, Toronto, Ontario M5S 3B2, Canada
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Teeratham Sivieng
aDepartment of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, 25 Willcocks St., University of Toronto, Toronto, Ontario M5S 3B2, Canada
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Hardeep Nahal
aDepartment of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, 25 Willcocks St., University of Toronto, Toronto, Ontario M5S 3B2, Canada
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  • ORCID record for Hardeep Nahal
Allison Gaudinier
bDepartment of Plant Biology and Genome Center, University of California, Davis, Davis, California 95616
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  • ORCID record for Allison Gaudinier
Asher Pasha
aDepartment of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, 25 Willcocks St., University of Toronto, Toronto, Ontario M5S 3B2, Canada
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Rose Oughtred
cInstitute for Biology I/Sammelbau Biologie II, RWTH Aachen University, Worringer Weg 3, 52074 Aachen, Germany
dIBG-2: Plant Sciences, Leo-Brandt-Strasse, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
eLewis-Sigler Institute for Integrative Genomics, Princeton University, Washington Road, Princeton, New Jersey 08544
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Kara Dolinski
cInstitute for Biology I/Sammelbau Biologie II, RWTH Aachen University, Worringer Weg 3, 52074 Aachen, Germany
dIBG-2: Plant Sciences, Leo-Brandt-Strasse, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
eLewis-Sigler Institute for Integrative Genomics, Princeton University, Washington Road, Princeton, New Jersey 08544
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Mike Tyers
fThe Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
gInstitute for Research in Immunology and Cancer, Université de Montréal, Montréal, Quebec H3C 3J7, Canada
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Siobhan M. Brady
bDepartment of Plant Biology and Genome Center, University of California, Davis, Davis, California 95616
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Ruth Grene
hDepartment of Plant Pathology, Physiology, and Weed Science, 101H Price Hall, Mail Code: 0331, 170 Drillfield Drive, Blacksburg, Virginia 24061
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Björn Usadel
cInstitute for Biology I/Sammelbau Biologie II, RWTH Aachen University, Worringer Weg 3, 52074 Aachen, Germany
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Nicholas J. Provart
aDepartment of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, 25 Willcocks St., University of Toronto, Toronto, Ontario M5S 3B2, Canada
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  • ORCID record for Nicholas J. Provart
  • For correspondence: nicholas.provart@utoronto.ca

Published April 2019. DOI: https://doi.org/10.1104/pp.18.01216

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  • © 2019 American Society of Plant Biologists. All Rights Reserved.

Abstract

Determining the complete Arabidopsis (Arabidopsis thaliana) protein-protein interaction network is essential for understanding the functional organization of the proteome. Numerous small-scale studies and a couple of large-scale ones have elucidated a fraction of the estimated 300,000 binary protein-protein interactions in Arabidopsis. In this study, we provide evidence that a docking algorithm has the ability to identify real interactions using both experimentally determined and predicted protein structures. We ranked 0.91 million interactions generated by all possible pairwise combinations of 1,346 predicted structure models from an Arabidopsis predicted “structure-ome” and found a significant enrichment of real interactions for the top-ranking predicted interactions, as shown by cosubcellular enrichment analysis and yeast two-hybrid validation. Our success rate for computationally predicted, structure-based interactions was 63% of the success rate for published interactions naively tested using the yeast two-hybrid system and 2.7 times better than for randomly picked pairs of proteins. This study provides another perspective in interactome exploration and biological network reconstruction using protein structural information. We have made these interactions freely accessible through an improved Arabidopsis Interactions Viewer and have created community tools for accessing these and ∼2.8 million other protein-protein and protein-DNA interactions for hypothesis generation by researchers worldwide. The Arabidopsis Interactions Viewer is freely available at http://bar.utoronto.ca/interactions2/.

  • Received October 2, 2018.
  • Accepted January 15, 2019.
  • Published January 24, 2019.

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Proteome-wide, Structure-Based Prediction of Protein-Protein Interactions/New Molecular Interactions Viewer
Shaowei Dong, Vincent Lau, Richard Song, Matthew Ierullo, Eddi Esteban, Yingzhou Wu, Teeratham Sivieng, Hardeep Nahal, Allison Gaudinier, Asher Pasha, Rose Oughtred, Kara Dolinski, Mike Tyers, Siobhan M. Brady, Ruth Grene, Björn Usadel, Nicholas J. Provart
Plant Physiology Apr 2019, 179 (4) 1893-1907; DOI: 10.1104/pp.18.01216

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Proteome-wide, Structure-Based Prediction of Protein-Protein Interactions/New Molecular Interactions Viewer
Shaowei Dong, Vincent Lau, Richard Song, Matthew Ierullo, Eddi Esteban, Yingzhou Wu, Teeratham Sivieng, Hardeep Nahal, Allison Gaudinier, Asher Pasha, Rose Oughtred, Kara Dolinski, Mike Tyers, Siobhan M. Brady, Ruth Grene, Björn Usadel, Nicholas J. Provart
Plant Physiology Apr 2019, 179 (4) 1893-1907; DOI: 10.1104/pp.18.01216
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Plant Physiology: 179 (4)
Plant Physiology
Vol. 179, Issue 4
Apr 2019
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