Www.e-nmr.eu Our mission Deploying and unifying the NMR e-Infrastructure in System Biology is to...
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www.e-nmr.eu Our mission Deploying and unifying the NMR e-Infrastructure in System Biology 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. ‘raw’ NMR data Recorded of biomolecular samples Result: e.g. structures of biomolecules Data analysis e.g. Structure calculation automated automated us r will allow researchers to enjoy all of the benefits of bio-NMR with only minimal efforts for the set-up of data analysis & calculations. e-nmr 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 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 Spronk NMR Consultancy, Vilnius, Lithuania European Bioinformatics Institute (EBI), Hinxton, UK Universite it Utrecht 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. 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!) 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: [email protected] HADDOCK statistics >500 registered users Server statistics > 110 registered users > 500 docking requests sinceJune 2008 Ported onto the e-NMRgrid infrastructure www.enmr.eu
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Transcript of Www.e-nmr.eu Our mission Deploying and unifying the NMR e-Infrastructure in System Biology is to...
www.e-nmr.eu Our mission Our mission
Deploying and unifying the NMR e-Infrastructure in System Biology
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.
‘raw’ NMR data
Recorded of biomolecular samples
Result:e.g. structures of biomolecules
Data analysis
e.g.Structure
calculation
automated automated
us rwill allow researchers to enjoy all of the benefits of bio-NMR with only minimal efforts for the set-up of data analysis & calculations.
e-nmr e-nmr
The e-nmr platform 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
Use the power of bio-NMR without the hassle of program installation, data format conversion, and protocol validation!
The team 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
Spronk NMR Consultancy, Vilnius, Lithuania
European Bioinformatics Institute (EBI), Hinxton, UK
UniversiteitUtrecht
Haddock 2.0 Haddock 2.0
new features, improved performance and a new GRID-based web serverBiomolecular 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.
Haddock 2.0 features 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!)
Sjoerd J. de Vries, Marc van Dijk, and Alexandre M.J.J. BonvinBijvoet Center for Biomolecular Research, Padualaan 8, 3584 CH Utrecht, The Netherlands.
Contact details: [email protected]
HADDOCK statistics
>500 registered users
Server statistics
> 110 registered users
> 500 docking requests sinceJune
2008
Ported onto the e-
NMRgrid infrastructure
www.enmr.eu
HADDOCK statistics
>500 registered users
Server statistics
> 110 registered users
> 500 docking requests sinceJune
2008
Ported onto the e-
NMRgrid infrastructure
www.enmr.eu
