1. 1. Introduction
2. 1. 1.1. HADDOCK - High Ambiguity Docking
   2. 1.2. Haddock3 modularity
3. 2. Installation
4. 1. 2.1. Virtual environments (conda / venv)
   2. 2.2. Obtaining HADDOCK
   3. 2.3. CNS
   4. 2.4. Using pre-installed containers
5. 3. Command Line Interfaces
6. 4. Preparing input files
7. 1. 4.1. Haddock3 requirements
   2. 4.2. Tools to manipulate structures
8. 5. Generating restraints for HADDOCK
9. 1. 5.1. Introduction to restraints in HADDOCK
   2. 5.2. Obtaining a set of interacting residues
   3. 5.3. The haddock3-restraints CLI
   4. 5.4. Automated restraints generation
   5. 1. 5.4.1. Symmetry restraints
      2. 5.4.2. DNA & RNA restraints
   6. 5.5. Ab-initio docking mode
   7. 5.6. Flexibility
10. 6. Generating a docking protocol
11. 1. 6.1. Global parameters
    2. 6.2. Concept of modules / parameters
    3. 6.3. Notable parameters
12. 7. Available modules
13. 1. 7.1. Topology
    2. 7.2. Sampling
    3. 7.3. Refinement
    4. 7.4. Scoring
    5. 7.5. Analysis
14. 8. Docking scenarios
15. 1. 8.1. Protein-protein docking
    2. 8.2. Protein-peptide docking
    3. 8.3. Protein-DNA docking
    4. 8.4. Antibody-antigen docking
    5. 8.5. Protein-glycan docking
    6. 8.6. Small-molecule docking
    7. 8.7. Complexes refinement protocols
    8. 8.8. Building cyclic peptide
    9. 8.9. Scoring workflow
    10. 8.10. Analysis pipelines
16. 9. Getting support / How to ask for help
17. 1. 9.1. Getting support / How to ask for help
    2. 9.2. FAQ
18. 10. Tutorials
19. 1. 10.1. Access to various tutorials
    2. 10.2. Best practice guide
    3. 1. 10.2.1. Structure preparation
       2. 10.2.2. Generating restraints
       3. 10.2.3. Small-molecules / Ligands
       4. 10.2.4. Glycans
       5. 10.2.5. Peptides
       6. 10.2.6. DNA / RNA
       7. 10.2.7. Proteins
       8. 10.2.8. Clustering complexes
       9. 10.2.9. Analysing results
20. 11. Haddock3 eco-system
21. 12. Online lectures
22. 13. Haddock3 source code
23. 14. How to cite haddock3
24. 1. 14.1. Citing haddock3
    2. 14.2. Haddock3-related publications
25. 15. Acknowledgements