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ProtoCaller: robust automation of binding free energy calculations

ProtoCaller: robust automation of binding free energy calculations
ProtoCaller: robust automation of binding free energy calculations
ProtoCaller is a Python library distributed through Anaconda which automates relative protein-ligand binding free energies in GROMACS. It links a number of popular specialized tools used to perform protein setup and parametrization, such as PDB2PQR, Modeller and AmberTools. ProtoCaller supports commonly used AMBER force fields with additional cofactor parameters, and AM1-BCC is used to derive ligand charges. ProtoCaller also comes with an extensive PDB parser, an enhanced maximum common substructure algorithm providing improved ligand-ligand mapping and a light GROMACS wrapper for running multiple molecular dynamics simulations. ProtoCaller is highly relevant to most researchers in the field of biomolecular simulation, allowing a customizable balance between automation and user intervention.
1549-9596
Suruzhon, Miroslav
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Senapathi, Tharindu
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Bodnarchuk, Michael S.
cb7c3390-a1e3-4e13-916c-200706d11f34
Viner, Russell
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Wall, Ian D.
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Barnett, Christopher B.
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Naidoo, Kevin J.
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Essex, Jonathan W.
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Suruzhon, Miroslav
4ea4dd8b-0a98-4598-9eaa-756d943b5dca
Senapathi, Tharindu
b98b7c07-a1c4-4ef2-9d9a-b44d71b25e7b
Bodnarchuk, Michael S.
cb7c3390-a1e3-4e13-916c-200706d11f34
Viner, Russell
d6d92ebc-31c4-4f0a-b655-ff291af3101c
Wall, Ian D.
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Barnett, Christopher B.
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Naidoo, Kevin J.
cad13bc7-b096-4c5d-b7a4-e4092e07dd3f
Essex, Jonathan W.
1f409cfe-6ba4-42e2-a0ab-a931826314b5

Suruzhon, Miroslav, Senapathi, Tharindu, Bodnarchuk, Michael S., Viner, Russell, Wall, Ian D., Barnett, Christopher B., Naidoo, Kevin J. and Essex, Jonathan W. (2020) ProtoCaller: robust automation of binding free energy calculations. Journal of Chemical Information and Modeling. (doi:10.1021/acs.jcim.9b01158).

Record type: Article

Abstract

ProtoCaller is a Python library distributed through Anaconda which automates relative protein-ligand binding free energies in GROMACS. It links a number of popular specialized tools used to perform protein setup and parametrization, such as PDB2PQR, Modeller and AmberTools. ProtoCaller supports commonly used AMBER force fields with additional cofactor parameters, and AM1-BCC is used to derive ligand charges. ProtoCaller also comes with an extensive PDB parser, an enhanced maximum common substructure algorithm providing improved ligand-ligand mapping and a light GROMACS wrapper for running multiple molecular dynamics simulations. ProtoCaller is highly relevant to most researchers in the field of biomolecular simulation, allowing a customizable balance between automation and user intervention.

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ProtoCaller_Main_Final_Revised_Clean - Accepted Manuscript
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Accepted/In Press date: 24 February 2020
e-pub ahead of print date: 24 February 2020

Identifiers

Local EPrints ID: 438452
URI: http://eprints.soton.ac.uk/id/eprint/438452
ISSN: 1549-9596
PURE UUID: e082f9d2-942a-4933-b9da-a3e36c288b43
ORCID for Jonathan W. Essex: ORCID iD orcid.org/0000-0003-2639-2746

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Date deposited: 10 Mar 2020 17:32
Last modified: 24 Feb 2021 05:01

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Contributors

Author: Miroslav Suruzhon
Author: Tharindu Senapathi
Author: Michael S. Bodnarchuk
Author: Russell Viner
Author: Ian D. Wall
Author: Christopher B. Barnett
Author: Kevin J. Naidoo

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