Combining Structural Modeling with Ensemble Machine Learning to Accurately Predict Protein Fold Stability and Binding Affinity Effects upon Mutation

Niklas Berliner; Joan Teyra; Recep Çolak; Sebastian Garcia Lopez; Philip M. Kim

doi:10.1371/journal.pone.0107353

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Peer-reviewed

Research Article

Combining Structural Modeling with Ensemble Machine Learning to Accurately Predict Protein Fold Stability and Binding Affinity Effects upon Mutation

Niklas Berliner ,

Contributed equally to this work with: Niklas Berliner, Joan Teyra, Recep Çolak

Affiliation Terrence Donnelly Centre for Cellular and Biomolecular Research (CCBR), University of Toronto, Toronto, Ontario, Canada
⨯
Joan Teyra ,

Contributed equally to this work with: Niklas Berliner, Joan Teyra, Recep Çolak

Affiliation Terrence Donnelly Centre for Cellular and Biomolecular Research (CCBR), University of Toronto, Toronto, Ontario, Canada
⨯
Recep Çolak ,

Contributed equally to this work with: Niklas Berliner, Joan Teyra, Recep Çolak

Affiliations Terrence Donnelly Centre for Cellular and Biomolecular Research (CCBR), University of Toronto, Toronto, Ontario, Canada, Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
⨯
Sebastian Garcia Lopez,

Affiliations Terrence Donnelly Centre for Cellular and Biomolecular Research (CCBR), University of Toronto, Toronto, Ontario, Canada, Universidad Nacional de Colombia, Manizales, Colombia
⨯
Philip M. Kim

* E-mail: pi@kimlab.org

Affiliations Terrence Donnelly Centre for Cellular and Biomolecular Research (CCBR), University of Toronto, Toronto, Ontario, Canada, Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada, Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
⨯

Combining Structural Modeling with Ensemble Machine Learning to Accurately Predict Protein Fold Stability and Binding Affinity Effects upon Mutation

Niklas Berliner,
Joan Teyra,
Recep Çolak,
Sebastian Garcia Lopez,
Philip M. Kim

Published: September 22, 2014
https://doi.org/10.1371/journal.pone.0107353

About the Authors

Niklas Berliner

Contributed equally to this work with: Niklas Berliner, Joan Teyra, Recep Çolak

Affiliation Terrence Donnelly Centre for Cellular and Biomolecular Research (CCBR), University of Toronto, Toronto, Ontario, Canada

Joan Teyra

Contributed equally to this work with: Niklas Berliner, Joan Teyra, Recep Çolak

Affiliation Terrence Donnelly Centre for Cellular and Biomolecular Research (CCBR), University of Toronto, Toronto, Ontario, Canada

Recep Çolak

Contributed equally to this work with: Niklas Berliner, Joan Teyra, Recep Çolak

Affiliations Terrence Donnelly Centre for Cellular and Biomolecular Research (CCBR), University of Toronto, Toronto, Ontario, Canada, Department of Computer Science, University of Toronto, Toronto, Ontario, Canada

Sebastian Garcia Lopez

Affiliations Terrence Donnelly Centre for Cellular and Biomolecular Research (CCBR), University of Toronto, Toronto, Ontario, Canada, Universidad Nacional de Colombia, Manizales, Colombia

Philip M. Kim

* E-mail: pi@kimlab.org

Affiliations Terrence Donnelly Centre for Cellular and Biomolecular Research (CCBR), University of Toronto, Toronto, Ontario, Canada, Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada, Department of Computer Science, University of Toronto, Toronto, Ontario, Canada

Competing Interests

The authors have declared that no competing interests exist.

Author Contributions

Conceived and designed the experiments: JT RC PMK. Performed the experiments: NB RC SGL. Analyzed the data: NB JT RC PMK. Wrote the paper: JT RC PMK.

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Protein structure prediction
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Protein domains
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Protein structure
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Point mutation
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Mutation databases
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Machine learning
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Protein structure databases
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Somatic mutation
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