An option to automatically pre-process input structures could be useful, e.g. to correct for ion namings, possible residue numbering overlap, residue insertions (e.g. in antibodies), or filtering of disordered regions for Alphafold models
In the current HADDOCK2 web server, prior to submitting a run users can download all pre-processed parameters and input data. Having an option to launch a local version of HADDOCK directly from those processed parameters would be nice.
In HADDOCK2.X we have introduced coarse-graining based on the Martini v2.2 force field. This feature is currently not available in HADDOCK3 and will need to be reimplemented. Further it would be interesting to investigate if a more flexible coarse-graining scheme would be possible (e.g. to have a coarser representation of molecules than the 4 to 1 mapping of Martini)
At the end of a docking workflow it would be nice to have statistics of the intermolecular contacts made between the various interfaces, reporting their nature (e.g. charged-charged, hydrogen bonds, hydrophobic) and visualising those in a matrix or circular plot form. This could be reported per cluster.