HADDOCK
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.
HADDOCK2.2 webserver
REGISTRATION: The use of the HADDOCK GRID-enabled docking server is free for academic users. Access to the server is managed through Single Sign On (SSO).
- HADDOCK server: the Easy interface
- HADDOCK server: the Prediction interface
- 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 server: the File upload interface
- HADDOCK server tool: generate AIR files for multibody docking
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 and a WIKI page to which you can contribute.
HADDOCK webserver statistics
Server statistics generated on: 2016-07-19 16:21:00
Number of running requests on Haddock: 3 , of which 2 are HADDOCK2.2 runs, and of which 3 on the WeNMR grid
Number of queued requests on Haddock: 2 of which 2 are HADDOCK2.2 runs
Total number of served requests as of June 1st 2008: 127834 , of which 44926 on the eNMR grid
Number of registered users: ( 6143 easy / 323 expert / 703 guru)
Number of registered users for the grid-enabled portal: 7572
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) and H2020 West-Life (project# 675858) European e-Infrastructure projects are acknowledged for the use of their web portals, which make use of the EGI infrastructure and DIRAC4EGI service with the dedicated support of CESNET-MetaCloud, INFN-PADOVA, NCG-INGRID-PT, RAL-LCG2, TW-NCHC, SURFsara and NIKHEF, and the additional support of the national GRID Initiatives of Belgium, France, Italy, Germany, the Netherlands, Poland, Portugal, Spain, UK, South Africa, Malaysia, Taiwan and the US Open Science Grid.”
- 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.
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
Server example
- HADDOCK basic protein-protein docking tutorial: A tutorial demonstrating the use of the HADDOCK web server to model a protein-protein complex using interface information derived from NMR chemical shift perturbation data. This tutorial does not require any Linux expertise and only makes use of our web server and PyMol for visualisation/analysis.
- HADDOCK ab-initio, multi-body symmetrical docking tutorial: A tutorial demonstrating multi-body docking with HADDOCK using its ab-initio mode with symmetry restraints. It is based on a former CASP-CAPRI target (T70).
- HADDOCK ligand binding site tutorial: A tutorial demonstrating the use of HADDOCK in ab-initio mode to screen for potential ligand binding sites. The information from the ab-initio run is then used to setup a binding pocket-targeted protein-ligand docking run. We use as example the multidrug exporter AcrB.
