This topic is dedicated to the BioExcel Summer School on Biomolecular Simulations 2018 Forum that takes place in Pula, Italy, on June 18-23 2018.
In this tutorial, we addressed the challenge of the molecular docking of covalent ligands. Using a covalent inhibitor of cathepsins as example, we showed the potential of HADDOCK, coupled with QM/MM calculations using CPMD, to reproduce the correct binding and get insights into the energetics of the binding.
You are welcome to post here any question, feedback, tip about software or methods related to this project. Note that you must be a member of the Integrative Modelling IG to post here, but all posts are public.