TIES20
TIES is a software to superimpose ligands for further analysis developed by UCL's Centre for Computational Science. They recently published the paper "TIES 20: Relative Binding Free Energy with a Flexible Superimposition Algorithm and Partial Ring Morphing" in the JCTC.
Getting started
- Go to ligands and generate the hybrids
- Simulate the hybrids with the ties_md package with support for NAMD or OpenMM
- Analyse the results with ties_ana
UCL's Centre for Computational Science
TIES was developed by Professor Peter Coveney's team at UCL's Centre for Computational Science.
Publications
Below are some other recent publications from the UCL Centre for Computational Sciences. To view a full list visit their website.
2021
- Bieniek, M. K., Bhati, A. P., Wan, S., & Coveney, P. V. (2021). TIES 20: Relative Binding Free Energy with a Flexible Superimposition Algorithm and Partial Ring Morphing. Journal of Chemical Theory and Computation, 17(2), 1250–1265. DOI:10.1021/acs.jctc.0c01179
- P. V. Coveney, D. Groen and A. G. Hoekstra, “Reliability and reproducibility in computational science: implementing validation, verification and uncertainty quantification in silico”, Phil. Trans. R. Soc. A. 379, 20200409 (2021), DOI:10.1098/rsta.2020.0409
- S. Wan, R. C. Sinclair and P. V. Coveney, “Uncertainty quantification in classical molecular dynamics”, Phil. Trans. R. Soc. A. 379, 20200082 (2021), DOI:10.1098/rsta.2020.0082
2017
- A. Bhati, S. Wan, D. Wright, P. V. Coveney, "Rapid, accurate, precise and reliable relative free energy prediction using ensemble based thermodynamic integration", Journal of Chemical Theory and Computation, 13 (1), 210–222 (2017), DOI: 10.1021/acs.jctc.6b00979
