SoftwareApplication
identifier: 10.5281/zenodo.6699227
name: haddock3
description: Haddock3 (High Ambiguity Driven protein-protein DOCKing) is a modular software for for the integrative modeling and refinement of biomolecular complexes.
description: # A brief introduction to HADDOCK3 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 parameterisable yet rigid simulation pipeline composed of three steps: `ridig-body docking (it0)`, `semi-flexible refinement (it1)`, and `final refinement (itw)`. ![HADDOCK 2.x workflow](https://github.com/haddocking/haddock3/raw/main/docs/figs/HADDOCK2-stages.png) 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. HADDOCK3 has therefore developed to truthfully work like a puzzle of many pieces (simulation modules) that users can combine freely. To this end, the “old” HADDOCK machinery has been modularised, and several new modules added, including third-party software. As a result, the modularisation achieved in HADDOCK3 allows users to duplicate steps within one workflow (e.g., to repeat the `it1` stage of the HADDOCK2.x rigid workflow). Note that, for simplification purposes, at this time, not all functionalities of HADDOCK2.x have been ported to HADDOCK3, which does not (yet) support NMR RDC, PCS and diffusion anisotropy restraints, cryo-EM restraints and coarse-graining. Any type of information that can be converted into ambiguous interaction restraints can, however, be used in HADDOCK3, which also supports the *ab initio* docking modes of HADDOCK. ![HADDOCK3 workflow](https://github.com/haddocking/haddock3/raw/main/docs/figs/HADDOCK3-workflow-scheme.png) To keep HADDOCK3's modules organised, we catalogued them into several categories. But, there are no constraints on piping modules of different categories. The main module's categories are "…
code repository: https://github.com/haddocking/haddock3
author: https://orcid.org/0000-0002-9113-0622
author: https://orcid.org/0000-0001-5267-3002
author: 0000-0002-2691-712X
author: https://orcid.org/0000-0001-9765-1261
author: https://orcid.org/0000-0002-5023-4601
author: https://orcid.org/0000-0001-8407-6472
author: Person
  given name: Charlotte
  family name: van Noort
  name: Charlotte van Noort
  affiliation: Organization
    name: Utrecht University
author: https://orcid.org/0000-0002-5821-2060
author: https://orcid.org/0000-0003-0594-0993
author: 0000-0001-5301-317X
author: Person
  given name: Regen
  family name: Tsai
  name: Regen Tsai
author: https://orcid.org/0000-0001-7369-1322
keywords: interactions
keywords: Inter-operability & linked data
keywords: Integrative modelling
keywords: modular
keywords: energetics
keywords: docking
keywords: biomolecular complexes
programming language: BitBake
programming language: C
programming language: C++
programming language: Dockerfile
programming language: Fortran
programming language: Jupyter Notebook
programming language: Lua
programming language: Pawn
programming language: Pep8
programming language: Prolog
programming language: Python
programming language: QMake
programming language: Roff
programming language: Shell
license:
  creative work: creativeWork
    name: Apache-2.0
reference publication: ja026939x
reference publication: nprot.2010.32
reference publication: j.jmb.2015.09.014
reference publication: s41596-024-01011-0
reference publication: btae583
reference publication: acs.jcim.5c00969

https://orcid.org/0000-0002-9113-0622
type: Person
given name: João
family name: M.C. Teixeira
name: João M.C. Teixeira
affiliation: Organization
  name: University of Padova

https://orcid.org/0000-0001-5267-3002
type: Person
given name: Rodrigo
family name: Vargas Honorato
name: Rodrigo Vargas Honorato
affiliation: Organization
  name: Utrecht University

0000-0002-2691-712X
type: Person
given name: Marco
family name: Giulini
name: Marco Giulini
affiliation: Organization
  name: Utrecht University

https://orcid.org/0000-0001-9765-1261
type: Person
given name: Brian
family name: Jimenez
name: Brian Jimenez
affiliation: Organization
  name: Zymvol Biomodeling

https://orcid.org/0000-0002-5023-4601
type: Person
given name: Barbara
family name: Vreede
name: Barbara Vreede
affiliation: Organization
  name: Netherlands eScience Center

https://orcid.org/0000-0001-8407-6472
type: Person
given name: Fakhereh
family name: (Sarah) Alidoost
name: Fakhereh (Sarah) Alidoost
affiliation: Organization
  name: Netherlands eScience Center

https://orcid.org/0000-0002-5821-2060
type: Person
given name: Stefan
family name: Verhoeven
name: Stefan Verhoeven
affiliation: Organization
  name: Netherlands eScience Center

https://orcid.org/0000-0003-0594-0993
type: Person
given name: Douwe
family name: Schulte
name: Douwe Schulte
affiliation: Organization
  name: Universiteit Utrecht

0000-0001-5301-317X
type: Person
given name: Victor
family name: Reys
name: Victor Reys
affiliation: Organization
  name: Utrecht University

https://orcid.org/0000-0001-7369-1322
type: Person
given name: Alexandre M.J.J.
family name: Bonvin
name: Alexandre M.J.J. Bonvin
affiliation: Organization
  name: Utrecht University

ja026939x
type: ScholarlyArticle
name: HADDOCK: A Protein−Protein Docking Approach Based on Biochemical or Biophysical Information
pagination: 1731-1737
url: https://doi.org/10.1021%2Fja026939x

nprot.2010.32
type: ScholarlyArticle
name: The HADDOCK web server for data-driven biomolecular docking
pagination: 883-897
url: https://doi.org/10.1038%2Fnprot.2010.32

j.jmb.2015.09.014
type: ScholarlyArticle
name: The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes
pagination: 720-725
url: https://doi.org/10.1016%2Fj.jmb.2015.09.014

s41596-024-01011-0
type: ScholarlyArticle
name: The HADDOCK2.4 web server for integrative modeling of biomolecular complexes
pagination: 3219-3241
url: https://doi.org/10.1038%2Fs41596-024-01011-0

btae583
type: ScholarlyArticle
name: Towards the accurate modelling of antibody−antigen complexes from sequence using machine learning and information-driven docking
url: https://doi.org/10.1093%2Fbioinformatics%2Fbtae583

acs.jcim.5c00969
type: ScholarlyArticle
name: HADDOCK3: A Modular and Versatile Platform for Integrative Modeling of Biomolecular Complexes
pagination: 7315-7324
url: https://doi.org/10.1021%2Facs.jcim.5c00969