1.
Introduction
1.1.
HADDOCK - High Ambiguity Docking
1.2.
Haddock3 modularity
2.
Installation
2.1.
Virtual environments (conda / venv)
2.2.
Obtaining HADDOCK
2.3.
CNS
2.4.
Using pre-installed containers
3.
Command Line Interfaces
4.
Preparing input files
4.1.
Haddock3 requirements
4.2.
Tools to manipulate structures
5.
Generating restraints for HADDOCK
5.1.
haddock3-restraints
5.2.
Automated restraints generation
5.2.1.
Symmetry restraints
5.2.2.
DNA & RNA restraints
5.3.
Ab-initio docking mode
5.4.
Flexibility
6.
Generating a docking protocol
6.1.
Global parameters
6.2.
Concept of modules / parameters
6.3.
Notable parameters
7.
Available modules
7.1.
Topology
7.2.
Sampling
7.3.
Refinement
7.4.
Scoring
7.5.
Analysis
8.
Docking scenarios
8.1.
Protein-protein docking
8.2.
Protein-peptide docking
8.3.
Protein-DNA docking
8.4.
Antibody-antigen docking
8.5.
Protein-glycan docking
8.6.
Small-molecule docking
8.7.
Complexes refinement protocols
8.8.
Building cyclic peptide
8.9.
Scoring workflow
8.10.
Analysis pipelines
9.
Getting support / How to ask for help
9.1.
Getting support / How to ask for help
9.2.
FAQ
10.
Tutorials
10.1.
Access to various tutorials
10.2.
Best practice guide
10.2.1.
Structure preparation
10.2.2.
Generating restraints
10.2.3.
Small-molecules / Ligands
10.2.4.
Glycans
10.2.5.
Peptides
10.2.6.
DNA / RNA
10.2.7.
Proteins
10.2.8.
Clustering complexes
10.2.9.
Analysing results
11.
Haddock3 eco-system
12.
Online lectures
13.
Haddock3 source code
14.
How to cite haddock3
14.1.
Citing haddock3
14.2.
Haddock3-related publications
15.
Acknowledgements
Light
Rust
Coal
Navy
Ayu
HADDOCK3 User Manual
Modules
More than 15 modules are currently available in HADDOCK3, grouped by category:
Topology
Sampling
Refinement
Scoring
Analysis