An interactive workflow for building user-defined congeneric series of ligands in protein binding pockets for input to free energy calculations.
Bieniek, Mateusz K., Ben Cree, Rachael Pirie, Joshua T. Horton, Natalie J. Tatum, and Daniel J. Cole. "An open-source molecular builder and free energy preparation workflow." Communications Chemistry 5, no. 1 (2022): 136.
https://doi.org/10.1038/s42004-022-00754-9
Please see cole-group.github.io/fegrow for full installation instructions, documentation and acknowledgements.
To get started see the online tutorial for which the IPython Notebook is available here.