A worldwide e-Infrastructure for NMR and structural biology

The WeNMR web Portals for Structural Biology

The web portals developed within WeNMR are among the most important elements of the project, as these form the points of entry for the end users. The ultimate goal is to offer to users registered with the eNMR/WeNMR Virtual Organization (VO) complete online protocols for processing NMR data, including all the steps depicted in Figure 1.

Fig. 1 NMR data processing from signal to 3D structure After acquisition of the primary NMR data, these are Fourier transformed to obtain spectra in which the individual frequency contributions or resonances of spin systems, and their relations, are revealed. The resonances subsequently have to be assigned to individual atoms. If sufficient resonances have been assigned, restraints can be inferred from the data, pertaining to distances between atoms, dihedral angles, domain orientations, etc. When an adequate number of restraints is available, these can be used to calculate a set of three-dimensional structures optimally satisfying these restraints. The resulting structures represent the structure of the protein in solution, which is validated against the available experimental data. Although the process is here depicted linearly, intermediate stages may involve iterative cycles of refinement.

In addition, each of these steps, and every program involved has value by itself as web based service. For this reason, a piece-wise implementation has been adopted and programs that are ported to the Grid are simultaneously being made available as a web portal. Currently, 12 portals are operational and can be accessed through http://www.wenmr.eu/wenmr/nmr-services. These provide access, among other services, to

  • HADDOCK for the prediction of biomolecular complexes
  • XPLOR-NIH
  • CYANA and CS-ROSETTA for calculating structures from NMR data
  • AMBER for structure refinement and molecular dynamics (MD) simulations
  • CcpNmr for data conversion
  • MARS for backbone assignment
  • TALOS+ for torsion angle prediction
  • MDDNMR for NUS spectral processing

Next to these available portals, several new ones are in development for various NMR applications, including the UNIO program that provides computational routines for each individual step depicted in Figure 1. 

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Cite WeNMR/WestLife

 
Usage of the WeNMR/WestLife 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.

EGI-approved

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

WestLife, the follow up project of WeNMR is a Virtual Research Environment e-Infrastructure project funded under Horizon 2020. Contract no. 675858

West-Life