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 energy calculations 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.
1917-1921
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.
059fa7bb-bde0-457f-8ba3-7e31cf72d3f1
Barnett, Christopher B.
77f80da6-e892-4bf5-841d-6d71b82b5b19
Naidoo, Kevin J.
cad13bc7-b096-4c5d-b7a4-e4092e07dd3f
Essex, Jonathan W.
1f409cfe-6ba4-42e2-a0ab-a931826314b5
27 April 2020
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.
059fa7bb-bde0-457f-8ba3-7e31cf72d3f1
Barnett, Christopher B.
77f80da6-e892-4bf5-841d-6d71b82b5b19
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, 60 (4), .
(doi:10.1021/acs.jcim.9b01158).
Abstract
ProtoCaller is a Python library distributed through Anaconda which automates relative protein-ligand binding free energy calculations 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.
Text
ProtoCaller_Main_Final_Revised_Clean
- Accepted Manuscript
More information
Accepted/In Press date: 24 February 2020
e-pub ahead of print date: 24 February 2020
Published date: 27 April 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
Catalogue record
Date deposited: 10 Mar 2020 17:32
Last modified: 06 Jun 2024 04:05
Export record
Altmetrics
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
Download statistics
Downloads from ePrints over the past year. Other digital versions may also be available to download e.g. from the publisher's website.
View more statistics
