Deploying and unifying the NMR
e-Infrastructure in System Biology
www.e-nmr.eu
 Our mission
is to make bio-NMR available to the scientific community in an integrated manner and
to significantly improve the time line from raw NMR data to final results.
us r
 e-nmr
will allow researchers to enjoy all of the benefits of bio-NMR with only minimal efforts for
the set-up of data analysis & calculations.
‘raw’ NMR data
Recorded of
biomolecular samples
automated
automated
e.g.
Structure
calculation
Result:
e.g. structures
of biomolecules
Data analysis
 The e-nmr platform
will be accessible through the web and will exploit GRID
technology to provide users with high computational capacity
and a secure protocol for access.
The platform will incorporate the majority of the software
tools currently in use within the bio-NMR community. Users can
request their favorite tools to be included.
Tutorials and standardized workflows will be provided
 Haddock 2.0
new features, improved performance and a new GRID-based web server
Biomolecular complexes are the molecular machines of the cell. In order to fully
understand how the various units work together to fulfill their tasks, structural
knowledge at atomic levelis required. Classical structural methods such as NMR and X-ray
crystallography can however encounter difficulties when dealing with such complexes. In
those cases, useful insights can be provided by computational approaches such as
docking, the process of predicting the structure of a complex based on its known
constituents.
HADDOCK is an information-driven docking method. Information on the interface regions
can be obtained from a variety of sources such as mutagenesis, mass spectrometry, NMR
and bioinformatic interface predictions. HADDOCK has been successfully applied to model
protein-protein, protein-DNA and protein-small molecule complexes, and has shown an
excellent performance in the CAPRI blind docking experiment.
Here we present the HADDOCK web server. The interface is user-friendly, requiring only
the structures of the individual components and a list of interacting residues. It deals
automatically with cofactors, ions and protonation states of histidines. A separate
interface allows the more advanced user to optimize the docking protocol for the system
under study. The HADDOCK server will open the modelling of biomolecular complexes
based on sparse information to a wide user community.
Use the power of bio-NMR without the hassle of
program installation, data format conversion, and
protocol validation!
 The team
Center for Biomolecular Magnetic Resonance
(BMRZ)JWG University, Frankfurt am Main, Germany
Magnetic Resonance Center (CERM)
University of Florence, Italy
National Institute of Nuclear Physics (INFN),
Padova, Italy
Bijvoet Center for Biomolecular Research (BCBR),
Utrecht University, The Netherlands
Universiteit
Utrecht
Spronk NMR Consultancy, Vilnius, Lithuania
European Bioinformatics Institute (EBI), Hinxton, UK
Sjoerd J. de Vries, Marc van Dijk, and Alexandre M.J.J. Bonvin
Bijvoet Center for Biomolecular Research, Padualaan 8, 3584 CH Utrecht, The Netherlands.
Contact details: a.m.j.j.bonvin@uu.nl
 Haddock 2.0 features
• Support protein-protein, protein-DNA and
protein-small molecule complexes
• Multi-body docking for up to six molecules
• Can deal with more kinds of experimental
data
• Ab-initio docking mode
• Improved scoring
• Solvated docking
• Freely obtainable for academic use
• Web server now open for the academic
community, running on a cluster of 176
2.33 GHz Xeon processors and on the eNMR
GRID (new!)