- 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
- The use of the HADDOCK WeNMR GRID-enabled docking server is
free for academic users. Access to the server is managed through Signle
Sign On 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 GROMACS web portal. Follow the instructions on screen. HADDOCK requires a valid X509 Grid certificate as explained below
- You have to be in possession of a valid X509 personal certificate that proves you are allowed to run calculations on the GRID and a membership of the eNMR Virtual Organization. If you do not yet have one you can find information on how to obtain a certificate here
- Once you are a member of the WeNMR VRC it is easy to subscribe to the many services WeNMR has to offer
- Note: registration does require a valid grid certificate!!!
-
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 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: 2013-05-21 10:22:58
- Number of running requests: 7 , of which 0 on the eNMR grid
- Number of queued requests: 3
- Total number of served requests as of June 1st 2008:
44056
,
of which 4762 on the eNMR grid - Number of registered users: 3062 ( 2428 easy / 227 expert / 408 guru)
- Number of registered users for the grid-enabled portal: 165
- 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 national GRID Initiatives of Belgium, France, Italy, Germany, the Netherlands (via the Dutch BiG Grid project), Portugal, Spain, UK, South Africa, Taiwan and the Latin America GRID infrastructure via the Gisela project is 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.
- Tutorials
- 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 tutorial movie is available here (requires Flash)
