- HADDOCK (High Ambiguity Driven protein-protein DOCKing) is an information-driven flexible docking approach for the modeling of biomolecular complexes. HADDOCK distinguishes itself from ab-initio docking methods in the fact that it encodes information from identified or predicted protein interfaces in ambiguous interaction restraints (AIRs) to drive the docking process. HADDOCK can deal with a large class of modeling problems including protein-protein, protein-nucleic acids and protein-ligand complexes.
- More information about HADDOCK2.2 can be found on the HADDOCK2.2 website
- Read also what an independent review by Moreira et al. has to say about our software...
- HADDOCK is one of the flagship software in the EU H2020 BioExcel
Center of Excellence for Biomolecular Research.
- The access of HADDOCK web server is free for non-profit users upon registration.
- Reference for use of the server
- G.C.P van Zundert, J.P.G.L.M. Rodrigues, M. Trellet, C. Schmitz, P.L. Kastritis, E. Karaca, A.S.J. Melquiond, M. van Dijk, S.J. de Vries and A.M.J.J. Bonvin (2016). "The HADDOCK2.2 webserver: User-friendly integrative modeling of biomolecular complexes." J. Mol. Biol., 428, 720-725 (2015).
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R. Vargas Honorato, P.I. Koukos, B. Jimenez-Garcia, A. Tsaregorodtsev, M. Verlato, A. Giachetti, A. Rosato and A.M.J.J. Bonvin (2021).
"Structural biology in the clouds: The WeNMR-EOSC Ecosystem."
Frontiers Mol. Biosci., 8, fmolb.2021.729513 (2021).
- HADDOCK2.2 webserver
- REGISTRATION: To use the HADDOCK docking server you must have registered for an account. If you do not have a account yet you can register here
- Note: The HADDOCK server might busy at times and/or closed to users because of workshops, tutorials or CAPRI runs. The Grid-enabled version of the HADDOCK server remains however always open.
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SERVICES:
- HADDOCK server: the Expert interface (requires Expert level access)
- HADDOCK server: the Refinement interface (requires Expert level access)
- HADDOCK server: the Guru interface (requires Guru level access)
- HADDOCK server: the Multi-body interface (requires Guru level access)
The default HADDOCK settings used by the server can be found here
A list of modified amino acids supported by HADDOCK can be found here
- HADDOCK help center
- You can post questions regarding the use of the HADDOCK web server using the BioExcel HADDOCK support center.
- Refer further to the online HADDOCK software page and its manual.
- The WeNMR site also provides a number of HADDOCK tutorials.
- HADDOCK webserver statistics
- Server statistics generated on: 2023-05-29 02:26:00
- Number of running requests on alcazar: 15 and of which 14 on the WeNMR/EOSC/EGI grid
- Number of requests being processed on alcazar: 0 of which 0 for the grid server
- Number of queued requests on alcazar: 18 of which 2 for the grid server
- Total number of served requests since June 1st 2008: 533585 , of which 361553 on the WeNMR grid
- Number of COVID-19 related served requests since April 1st 2020: 75474
- For more statistics including HADDOCK2.4 see here
- Server example
- An example of the server output for the e2a-hpr example provided with the HADDOCK distribution can be found here. This is the result of the E2A-HPr demo run below via the "easy interface" using only chemical shift perturbations.
- Tutorials
- A demo web form for the easy interface with pre-loaded parameters is available here.
It corresponds to the E2A-HPR docking example based on NMR chemical shift perturbations.
Various tutorials describing the use of the HADDOCK web portal with various combinations of data are available here
A demo of the easy interface based on the above tutorial is available in YouTube, together with a 3 hour recent lecture on HADDOCK by Prof. A. Bonvin
And finally a SBGrid webinar by Prof. A. Bonvin describing the differences between using the webserver and a local version of HADDOCK is available on YouTube
- Research
- Research within the computational structural biology group focuses on the development of reliable bioinformatic and computational approaches to predict, model and dissect biomolecular interactions at atomic level. For this, bioinformatic data, structural information and available biochemical or biophysical experimental data are combined to drive the modelling process. By following a holistic approach integrating various experimental information sources with computational structural biology methods we aim at obtaining a comprehensive description of the structural and dynamic landscape of complex biomolecular machines, adding the structural dimension to interaction networks and opening the route to systematic and genome-wide studies of biomolecular interactions.
- Learn more >>
- World map:
- Links:
- NMR Spectroscopy >>
The servers home, the NMR Spectroscopy Department - Bijvoet Center >>
The Bijvoet-Center for structural biology - Faculty of
Science >>
Faculty of Science main page - Utrecht University >>
Utrecht University main page - Integrative Modelling IG >>
Integrative Modelling Interest Group
