e-nmr.eu

1. us r automated automated Deploying and unifying the NMR e-Infrastructure in System Biology Our mission www.e-nmr.eu 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. 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 e.g. Structure calculation Result: e.g. structures of biomolecules Data analysis The e-nmr platform Haddock 2.0 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 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. HADDOCKis 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 Haddock 2.0 features 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 HADDOCK statistics >500 registered users Server statistics > 110 registered users > 500 docking requests sinceJune 2008 Ported onto the e-NMRgrid infrastructure www.enmr.eu • Support protein-protein, protein-DNAand 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!) Universiteit Utrecht 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