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DINC-COVID: A webserver for ensemble docking with flexible SARS-CoV-2 proteins

View ORCID ProfileSarah Hall-Swan, View ORCID ProfileDinler A. Antunes, View ORCID ProfileDidier Devaurs, View ORCID ProfileMauricio M. Rigo, View ORCID ProfileLydia E. Kavraki, View ORCID ProfileGeancarlo Zanatta
doi: https://doi.org/10.1101/2021.01.21.427315
Sarah Hall-Swan
1Department of Computer Science, Rice University, Houston, Texas, 77005, United States
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Dinler A. Antunes
1Department of Computer Science, Rice University, Houston, Texas, 77005, United States
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Didier Devaurs
2Univ. Grenoble Alpes, CNRS, Inria, Grenoble INP, LJK, 38000 Grenoble, France
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Mauricio M. Rigo
1Department of Computer Science, Rice University, Houston, Texas, 77005, United States
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Lydia E. Kavraki
1Department of Computer Science, Rice University, Houston, Texas, 77005, United States
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  • For correspondence: geancarlo.zanatta@ufc.br
Geancarlo Zanatta
3Department of Physics, Federal University of Ceará, Fortaleza-CE, Brazil
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  • ORCID record for Geancarlo Zanatta
  • For correspondence: geancarlo.zanatta@ufc.br
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Abstract

Motivation Recent efforts to computationally identify inhibitors for SARS-CoV-2 proteins have largely ignored the issue of receptor flexibility. We have implemented a computational tool for ensemble docking with the SARS-CoV-2 proteins, including the main protease (Mpro), papain-like protease (PLpro) and RNA-dependent RNA polymerase (RdRp).

Results Ensembles of other SARS-CoV-2 proteins are being prepared and made available through a user-friendly docking interface. Plausible binding modes between conformations of a selected ensemble and an uploaded ligand are generated by DINC, our parallelized meta-docking tool. Binding modes are scored with three scoring functions, and account for the flexibility of both the ligand and receptor. Additional details on our methods are provided in the supplementary material.

Availability dinc-covid.kavrakilab.org

Supplementary information Details on methods for ensemble generation and docking are provided as supplementary data online.

Contact geancarlo.zanatta{at}ufc.br, kavraki{at}rice.edu

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted January 22, 2021.
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DINC-COVID: A webserver for ensemble docking with flexible SARS-CoV-2 proteins
Sarah Hall-Swan, Dinler A. Antunes, Didier Devaurs, Mauricio M. Rigo, Lydia E. Kavraki, Geancarlo Zanatta
bioRxiv 2021.01.21.427315; doi: https://doi.org/10.1101/2021.01.21.427315
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DINC-COVID: A webserver for ensemble docking with flexible SARS-CoV-2 proteins
Sarah Hall-Swan, Dinler A. Antunes, Didier Devaurs, Mauricio M. Rigo, Lydia E. Kavraki, Geancarlo Zanatta
bioRxiv 2021.01.21.427315; doi: https://doi.org/10.1101/2021.01.21.427315

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