A worldwide e-Infrastructure for NMR and structural biology

HADDOCK2.2 release

We are glad to officially release version 2.2 of HADDOCK. For general information and the online manual refer to:

 
 
 
The main changes with respect to version 2.1 are:
 
  • Default setup (parameters/topology files) for CNS1.3
  • New S3 and C4 symmetry restraints 
  • Radius of gyration restraint
  • Option to automatically define backbone dihedral angle restraints from the input structures
  • Pseudo contact shift restraints (CNS must be recompiled with the provided routines)
  • Interaction matrix to scale down or turn off interactions between specific molecules
  • Water-mediated contact probabilities option based on Kyte-Doolittle hydrophobic scale
  • DNA-specific fraction of water to keep for solvated docking
  • Fraction of common contact (FCC) clustering option
  • Added examples for various docking scenarios (see the example directory)
 
 
Users with a local installation of HADDOCK can simply request the software by emailing Prof. Bonvin, indicating the name of the PI registered for HADDOCK. New users should fill in a license form. See for this:
 
 
 
HADDOCK2.2 is also available as web portal. Users already having login credentials for the HADDOCK portal can directly start to use it. New users should register for an account. See:
 
 
(also accessible from the NMR menu -> modelling  on the WeNMR web site).
 
(Note that the old 2.1 portal remains accessible at its current URL)
 
In principle, the 2.2 portal should accept old parameter files saved from the 2.1 version (but make sure the run name does not contain any punctuations or spaces).
 
With best regards
Alexandre & HADDOCK team
 

Cite WeNMR

 
Usage of the WeNMR portals should be acknowledged in any publication:
 
"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."
 
And the following article describing the WeNMR portals should be cited:
Wassenaar et al. (2012). WeNMR: Structural Biology on the Grid.J. Grid. Comp., 10:743-767.

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The WeNMR Virtual Research Community has been the first to be officially recognized by the EGI.

European Union

WeNMR is an e-Infrastructure project funded under the 7th framework of the EU. Contract no. 261572