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

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

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 thoroughl...

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Veröffentlicht in:Journal of chemical information and modeling 2023-02, Vol.63 (3), p.718-724
Hauptverfasser: Bieniek, Mateusz K., Wade, Alexander D., Bhati, Agastya P., Wan, Shunzhou, Coveney, Peter V.
Format: Artikel
Sprache:eng
Schlagworte:
Application Note
Binding
Binding energy
Chemistry
Computer Science
Drug Discovery
Free energy
Freeware
Mathematical analysis
Molecular dynamics
Molecular Dynamics Simulation
Open source software
Pharmacology & Pharmacy
Software
Thermodynamics
Topology
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Beschreibung
Zusammenfassung: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.
ISSN:1549-9596
1549-960X
DOI:10.1021/acs.jcim.2c01596