Development priorities based on user feedback
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
We are working on a new version of the server, keep the code in line with HADDOCK3 for what concerns parameters (e.g. improved support for glycans), but won’t have any major updates.
Development priorities based on user feedback
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 is being reimplemented. We also plan to provide support for the latest Martini force field.
Follow the developments in our GitHub repository (CG-HADDOCK branch)
From the 2024 BioExcel survey, HADDOCK users indicated a need for improved support for protein-glycan modelling. We will extend the support for various carbohydrates and develop protocols for efficient protein-glycans docking.
Extended support for glycans was added in the following pull request.
A protocol for protein-glycan docking was recently published: DOI: 10.1021/acs.jcim.4c01372
From the 2024 BioExcel survey, HADDOCK users indicated a need for improved protocols for modelling anti/nanobody complexes, including the use of AI tools. This
A protocol for antibody-antigen modelling, using AI-generated models as input for the docking was recently published: DOI:10.1093/bioinformatics/btae583 . Tutorials on antibody-antigen modelling are available from the HADDOCK3 tutorial page. Work on nanobodies is ongoing.
Implemented features based on user feedback
Following user requirements, a contactmap analysis module was develop to analyse the intermolecular contacts made between the various interfaces, reporting on their nature (e.g. charged-charged, hydrogen bonds, hydrophobic) and visualising those in a matrix or circular plot form.
All related developments can be found in our GitHub repository searching with the label “m|Contacmap”
Following user requirements, HADDOCK3 now produces easy to read analysis reports with all cluster statistics and visualisation of results as done on the HADDOCK2 web server.
All related developments can be found in our GitHub repository searching with the label “analysis/postprocessing”
This new module enables an automated alanine scanning of all interface residues to dissect the contribution of each residue to the interaction energetics. Custom mutations to any other amino acid types are also supported.
All related developments can be found in our GitHub repository searching with the label “m|alascan”
