TIES 2.0: A Dual-Topology Open Source Relative Binding Free Energy Builder with Web Portal

[Image: see text] Relative binding free energy (RBFE) calculations are widely used to aid the process of drug discovery. TIES, Thermodynamic Integration with Enhanced Sampling, is a dual-topology approach to RBFE calculations with support for NAMD and OpenMM molecular dynamics engines. The software...

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Autores principales: Bieniek, Mateusz K., Wade, Alexander D., Bhati, Agastya P., Wan, Shunzhou, Coveney, Peter V.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Chemical Society 2023
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9930115/
https://www.ncbi.nlm.nih.gov/pubmed/36719676
http://dx.doi.org/10.1021/acs.jcim.2c01596
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author Bieniek, Mateusz K.
Wade, Alexander D.
Bhati, Agastya P.
Wan, Shunzhou
Coveney, Peter V.
author_facet Bieniek, Mateusz K.
Wade, Alexander D.
Bhati, Agastya P.
Wan, Shunzhou
Coveney, Peter V.
author_sort Bieniek, Mateusz K.
collection PubMed
description [Image: see text] Relative binding free energy (RBFE) calculations are widely used to aid the process of drug discovery. TIES, Thermodynamic Integration with Enhanced Sampling, is a dual-topology approach to RBFE calculations with support for NAMD and OpenMM molecular dynamics engines. The software has been thoroughly validated on publicly available datasets. Here we describe the open source software along with a web portal (https://ccs-ties.org) that enables users to perform such calculations correctly and rapidly.
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spelling pubmed-99301152023-02-16 TIES 2.0: A Dual-Topology Open Source Relative Binding Free Energy Builder with Web Portal Bieniek, Mateusz K. Wade, Alexander D. Bhati, Agastya P. Wan, Shunzhou Coveney, Peter V. J Chem Inf Model [Image: see text] Relative binding free energy (RBFE) calculations are widely used to aid the process of drug discovery. TIES, Thermodynamic Integration with Enhanced Sampling, is a dual-topology approach to RBFE calculations with support for NAMD and OpenMM molecular dynamics engines. The software has been thoroughly validated on publicly available datasets. Here we describe the open source software along with a web portal (https://ccs-ties.org) that enables users to perform such calculations correctly and rapidly. American Chemical Society 2023-01-31 /pmc/articles/PMC9930115/ /pubmed/36719676 http://dx.doi.org/10.1021/acs.jcim.2c01596 Text en © 2023 The Authors. Published by American Chemical Society https://creativecommons.org/licenses/by/4.0/Permits the broadest form of re-use including for commercial purposes, provided that author attribution and integrity are maintained (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Bieniek, Mateusz K.
Wade, Alexander D.
Bhati, Agastya P.
Wan, Shunzhou
Coveney, Peter V.
TIES 2.0: A Dual-Topology Open Source Relative Binding Free Energy Builder with Web Portal
title TIES 2.0: A Dual-Topology Open Source Relative Binding Free Energy Builder with Web Portal
title_full TIES 2.0: A Dual-Topology Open Source Relative Binding Free Energy Builder with Web Portal
title_fullStr TIES 2.0: A Dual-Topology Open Source Relative Binding Free Energy Builder with Web Portal
title_full_unstemmed TIES 2.0: A Dual-Topology Open Source Relative Binding Free Energy Builder with Web Portal
title_short TIES 2.0: A Dual-Topology Open Source Relative Binding Free Energy Builder with Web Portal
title_sort ties 2.0: a dual-topology open source relative binding free energy builder with web portal
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9930115/
https://www.ncbi.nlm.nih.gov/pubmed/36719676
http://dx.doi.org/10.1021/acs.jcim.2c01596
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