Haddock3 eco-system

Haddock3 can be used together with other tools that have been developed and maintained by the BonvinLab.

Local installation of tools

Here are some useful links to software that can be useful to solve your research question:

  • pdb-tools: A dependency-free cross-platform swiss army knife for PDB files.
  • prodigy: Predict the binding affinity of protein-protein and protein-ligand complexes from structural data
  • arctic3d: Automatic Retrieval and ClusTering of Interfaces in Complexes from 3D structural information
  • proABC-2: Deep learning framework to predict antibody paratope residues
  • DisVis: Visualisation of conformational space restriction by distance restraints
  • DeepRank-GNN-ESM: Deep learning framework for scroing protein-protein interaction docking poses.

Useful utilities

  • haddock-restraints: Generate distance restraints to be used in HADDOCK
  • haddock-runner: Run large scale HADDOCK simulations using multiple input molecules in different scenarios
  • haddock-tools: Set of useful utility scripts developed by the BonvinLab group members
  • haddock-mmcif: Encode information from a HADDOCK run to a cif file to be deposited in PDB-Dev

Webservers

We also provide online resources to perform computations related to the tools we developed.

Access our web portal here: https://wenmr.science.uu.nl/.

Haddock3 Web-Application

Here is the GitHub repository of the haddock3 web applications.