- 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 HADDOCK can be found on the HADDOCK website
- Read also what an independent review by Moreira et al. has to say about our software...
- HADDOCK webserver
- REGISTRATION: The use of the HADDOCK WeNMR GRID-enabled docking server is
free for academic users. Access to the server is managed through Single
Sign On (SSO) authentication using your WeNMR account. Old style HADDOCK web
server accounts are still supported. How to proceed:
- Become a member of the WeNMR Virtual Research Community at www.wenmr.eu
- Once logged in, go to the "My Services" tab in your account profile and subscribe to the HADDOCK web portal. Follow the instructions on screen.
- Once you are a member of the WeNMR VRC it is easy to subscribe to the many services WeNMR has to offer, some of which will however require a valid X509 personal certificate
- HADDOCK help center
- You can post question regarding the use of the HADDOCK web server using the WeNMR HADDOCK support center. To make use of this service you should first register with the WeNMR virtual research community (register link on the top right of the WeNMR page).
- Further the WeNMR site also provides a number of HADDOCK tutorials and a WIKI page to which you can contribute.
- HADDOCK webserver statistics
- Server statistics generated on: 2013-12-07 15:05:47
- Number of running requests: 10, of which 10 on the eNMR grid
- Number of queued requests: 0
- Total number of served requests as of June 1st 2008:
of which 5331 on the eNMR grid
- Number of registered users: 3454 ( 2792 easy / 232 expert / 431 guru)
- Number of registered users for the grid-enabled portal: 3454
- Note that another local cluster is also used and the reported cluster load does only represent the HADDOCK cluster.
- References for use of the WeNMR GRID-enabled server
S.J. de Vries, M. van Dijk and A.M.J.J. Bonvin
"The HADDOCK web server for data-driven biomolecular docking."
Nature Protocols, 5, 883-897 (2010).
T.A. Wassenaar, M. van Dijk, N. Loureiro-Ferreira, G. van der Schot, S.J. de Vries, C. Schmitz, J. van der Zwan, R. Boelens, A. Giachetti, L. Ferella, A. Rosato, I. Bertini, T. Herrmann, H.R.A. Jonker, A. Bagaria, V. Jaravine, P. Guntert, H. Schwalbe, W.F. Vranken, J.F. Doreleijers, G. Vriend, G.W. Vuister, D. Franke, A. Kikhney, D.I. Svergun, R. Fogh, J. Ionides, E.D. Laue, C. Spronk, S. Jurka, M. Verlato, S. Badoer, S. Dal Pra, M. Mazzucato, E. Frizziero and A.M.J.J. Bonvin
"WeNMR: Structural Biology on the Grid."
J. Grid. Comp., 10, 743-767 (2012).
- And add in addition the following text to the acknowledgment section:
"The WeNMR project (European FP7 e-Infrastructure grant, contract no. 261572, www.wenmr.eu), supported by the European Grid Initiative (EGI) through the national GRID Initiatives of Belgium, France, Italy, Germany, the Netherlands, Poland, Portugal, Spain, UK, South Africa, Malaysia, Taiwan, the Latin America GRID infrastructure via the Gisela project and the US Open Science Grid (OSG) are acknowledged for the use of web portals, computing and storage facilities."
- Server output 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 a run via the "easy interface" using only chemical shift perturbations as defined in the HADDOCK tutorial.
- A demo web form for the easy interface with pre-loaded parameters is available here
A demo web form for the guru interface with pre-loaded parameters is available here
A tutorial describing the use of the HADDOCK web portal with various combinations of data is available here
A demo of the easy interface based on the above tutorial is available in YouTube, together with a 1 1/2 hour lecture on HADDOCK by Prof. A. Bonvin
An old tutorial movie is available here (requires Flash)