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

Mateusz K BieniekAlexander D WadeAgastya P BhatiShunzhou Wan Peter V Coveney

Published in: Journal of chemical information and modeling (2023)

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.

Keyphrases

molecular dynamics
density functional theory
drug discovery
dna binding
data analysis
rna seq
molecular dynamics simulations
single cell