HADDOCK is a versatile and information-driven docking tool that can integrate data from various biochemical, biophysical, and bioinformatics methods to enhance sampling, scoring, or both. It is different from other docking software by its ability (inherited from CNS) to efficiently incorporate experimental data used as restraints, called Ambiguous Interaction Restraints (AIRs), to guide the docking process alongside traditional energetics and shape complementarity. AIRs are defined through a list of residues that are categorized as active or passive, and the scoring function is adjusted based on the presence or absence of these residues in the interface.
The HADDOCK software distribution and webserver can be accessed free of charge by non-commercial users. Currently, multiple versions of HADDOCK are co-existing. The latest stable version of HADDOCK (2.4) can be downloaded or accessed through a user-friendly web interface. HADDOCK3 is the next generation integrative modelling software in the long-lasting HADDOCK project. It represents a complete rethinking and rewriting of the HADDOCK2.x series, implementing a new way to interact with HADDOCK and offering new features to users who can now define custom workflows. In the previous HADDOCK2.x versions, users had access to a highly parametrisable yet rigid simulation pipeline composed of three steps: rigid-body docking (it0), semi-flexible refinement (it1), and final refinement (itw). In HADDOCK3, users have the freedom to configure docking workflows into functional pipelines by combining the different HADDOCK3 modules, thus adapting the workflows to their projects.
HADDOCK versions are under active development, considering user feedback to prioritise developments based on identified needs with the potential for large scientific/industrial impact. Therefore, upcoming web interface and new modules for HADDOCK3 are under progress.
The new HADDOCK3 design now enables researchers to configure diverse scenarios and tailor their workflows based on specific research questions and objectives. To achieve this modularity, HADDOCK3 consists of modules that can be combined at will into custom pipelines. Currently, the available modules are grouped in five main categories: topology, sampling, refinement, scoring and analysis.
Whether you are new to HADDOCK or you already have some experience, we have collated a number of relevant learning and support resources to help you out. Access the HADDOCK documentation, dedicated support forum, lectures, tutorials and more!