- 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
-
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.
- HADDOCK webserver statistics
- Server statistics generated on: 2023-05-29 02:39:09
- 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: 533586 , 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
- 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 A.M.J.J. Bonvin (2016). "The HADDOCK2.2 webserver: User-friendly integrative modeling of biomolecular complexes." J. Mol. Biol., 428, 720-725 (2015).
- 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).
- 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-LNL-2, NCG-INGRID-PT, TW-NCHC, CESGA, IFCA-LCG2, UA-BITP, TR-FC1-ULAKBIM, CSTCLOUD-EGI, IN2P3-CPPM, 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.
- 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 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
- This work is co-funded by the Horizon 2020 projects EOSC-hub (grant number 777536) and BioExcel (grant numbers 823830 and 675728) and by a computing grant from NWO-ENW (project number 2019.053).
