Accelerating Alchemical Free Energy Prediction Using a Multistate Method: Application to Multiple Kinases

This release corresponds to a version of the re-eds pipeline which can reproduce the results of the publication:

J. Chem. Inf. Model. 2023, 63, 22, 7133–7147
DOI: https://pubs.acs.org/doi/full/10.1021/acs.jcim.3c01469

Free Energies of Water Replacement with RE-EDS

Water sites RE-EDS version used in Accounting for Solvation Correlation Effects on the Thermodynamics of Water Networks in Protein Cavities; Emilia P. Barros, Benjamin Ries, Candide Champion, Salomé R. Rieder, Sereina Riniker

An Automatized RE-EDS Sampling Procedure

Version 1.0 - used in:

• RestraintMaker: a graph-based approach to select distance restraints in free-energy calculations with dual topology; Benjamin Ries^, Salomé Rieder^, Clemens Rhiner, Philippe H. Hünenberger and Sereina Riniker (2022).
• Relative Free-Energy Calculations for Scaffold Hopping-Type Transformations with an Automated RE-EDS Sampling Procedure; Benjamin Ries, Karl Normak, R.Gregor Weiß, Salomé Rieder, Emília P. Barros, Candide Champion, Gerhard König, Sereina Riniker (2022)

reeds

Merge pull request #44 from rinikerlab/new_exchanges

Added a new plot type for plotting exchange frequencies.