- 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.
- HADDOCK webserver
- REGISTRATION: The use of the HADDOCK WeNMR GRID-enabled docking server is
free for academic users. How to proceed:
- Then register here for HADDOCK access
- 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)
- 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.
- HADDOCK webserver statistics
- Server statistics generated on: 2021-06-13 13:16:33
- Number of running requests on alcazar: and of which on the WeNMR/EOSC/EGI grid
- Number of requests being processed on alcazar: of which for the grid server
- Number of queued requests on alcazar: of which for the grid server
- Total number of served requests since June 1st 2008: 349855 , of which 198742 on the WeNMR grid
- Number of COVID-19 related served requests since April 1st 2020: 30170
- For more statistics including HADDOCK2.4 see here
- References for use of the WeNMR GRID-enabled 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 (2016).
"The HADDOCK2.2 webserver: User-friendly integrative modeling of biomolecular complexes."
J. Mol. Biol., 428, 720-725 (2015).
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 FP7 WeNMR (project# 261572), H2020 West-Life (project# 675858), EOSC-hub (project# 777536) and the EGI-ACE (project# 101017567) European e-Infrastructure projects are acknowledged for the use of their web portals, which make use of the EGI infrastructure with the dedicated support of CESNET-MCC, INFN-PADOVA-STACK, INFN-LNL-2, NCG-INGRID-PT, TW-NCHC, CESGA, IFCA-LCG2, UA-BITP, SURFsara and NIKHEF, and the additional support of the national GRID Initiatives of Belgium, France, Italy, Germany, the Netherlands, Poland, Portugal, Spain, UK, Taiwan and the US Open Science Grid."
- 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.
- 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 recent 3 hour 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