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DLA-Ranker: Evaluating protein docking conformations with many locally oriented cubes

View ORCID ProfileYasser Mohseni Behbahani, View ORCID ProfileÉlodie Laine, View ORCID ProfileAlessandra Carbone
doi: https://doi.org/10.1101/2021.10.26.465898
Yasser Mohseni Behbahani
Laboratory of Computational and Quantitative Biology (LCQB), UMR 7238, Sorbonne Université, CNRS, IBPS, Paris, 75005, France
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  • ORCID record for Yasser Mohseni Behbahani
Élodie Laine
Laboratory of Computational and Quantitative Biology (LCQB), UMR 7238, Sorbonne Université, CNRS, IBPS, Paris, 75005, France
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  • For correspondence: elodie.laine@sorbonne-universite.fr alessandra.carbone@sorbonne-universite.fr
Alessandra Carbone
Laboratory of Computational and Quantitative Biology (LCQB), UMR 7238, Sorbonne Université, CNRS, IBPS, Paris, 75005, France
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  • For correspondence: elodie.laine@sorbonne-universite.fr alessandra.carbone@sorbonne-universite.fr
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Abstract

Proteins ensure their biological functions by interacting with each other, and with other molecules. Determining the relative position and orientation of protein partners in a complex remains challenging. Here, we address the problem of ranking candidate complex conformations toward identifying near-native conformations. We propose a deep learning approach relying on a local representation of the protein interface with an explicit account of its geometry. We show that the method is able to recognise certain pattern distributions in specific locations of the interface. We compare and combine it with a physics-based scoring function and a statistical pair potential.

Competing Interest Statement

The authors have declared no competing interest.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted October 28, 2021.
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DLA-Ranker: Evaluating protein docking conformations with many locally oriented cubes
Yasser Mohseni Behbahani, Élodie Laine, Alessandra Carbone
bioRxiv 2021.10.26.465898; doi: https://doi.org/10.1101/2021.10.26.465898
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DLA-Ranker: Evaluating protein docking conformations with many locally oriented cubes
Yasser Mohseni Behbahani, Élodie Laine, Alessandra Carbone
bioRxiv 2021.10.26.465898; doi: https://doi.org/10.1101/2021.10.26.465898

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