Related Experiment Video
Updated: Aug 12, 2025
Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
Published on: July 16, 2017
TIES 2.0: A Dual-Topology Open Source Relative Binding Free Energy Builder with Web Portal
Mateusz K Bieniek1,2, Alexander D Wade1, Agastya P Bhati1
1Centre for Computational Science, Department of Chemistry, University College London, London WC1H 0AJ, United Kingdom.
Abstract:
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.
More Related Videos
Related Concept Videos
00:49Ligand Binding and Linkage
01:49Conserved Binding Sites
02:40Ligand Binding Sites
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
02:18The Equilibrium Binding Constant and Binding Strength
02:13Cooperative Binding of Transcription Regulators
01:57Protein Complexes with Interchangeable Parts
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order...