Our partnership with @boehringerglobal.bsky.social has been very productive. Last year, Benjamin Ries published scientific papers describing two different tools for setting up alchemical simulations, that he built as a contributor to our team. These tools are now integral to our RBFE protocol.
pubs.acs.org
Konnektor: A Framework for Using Graph Theory to Plan Networks for Free Energy Calculations
Alchemical free energy campaigns can be planned using graph theory by building networks that contain nodes representing molecules that are connected by possible transformations as edges. We introduce ...