A worldwide e-Infrastructure for NMR and structural biology

NMR Services

Our NMR web portals provide access to many of the powerful software packages ported by the e-NMR and WeNMR consortia to the GRID. A wide range of structural biology related software packages are available covering the many stages in NMR structure calculation, molecular dynamics simulations and structure modelling.

Assignment

  • Auto Assign
    AutoAssign is a constraint-based expert system for automating the analysis of backbone resonance assignments using triple resonance NMR spectra of small proteins. 

  • MARS
    MARS is a program for robust automatic backbone assignment of 13C/15N labeled proteins.

  • UNIO
    The UNIO program enables you to perform automated NMR data analysis and structure calculation for 3D protein structure determination. 

Analysis

  • TALOS+
    is a program which predicts torsion angles using information derived from chemical shift, amino acid type, and the area of the Ramachandran map where the residue is likely to reside in. 

  • AnisoFIT
    allows users to fit pseudocontact shift and/or residual dipolar couplings of a protein against its structure, and can be used to determine the magnetic susceptibility tensor anisotropy or the anisotropy of the diffusion tensor.  

  • MaxOcc
    MaxOcc can be used to make rigorous numerical assessments about the maximum percent of time that a conformer of a flexible macromolecule can exist and still be compatible with the experimental data.

  • iCing
    iCing is the webinterface to the NMR structure and data validation software suite CING .  

Structure Calculation

  • CS-ROSETTA
    CS-ROSETTA is a protocol which generates 3D models of proteins, using only the 13CA, 13CB, 13C', 15N, 1HA and 1HN NMR chemical shifts as input. 

  • ARIA
    Allows for automated nuclear magnetic resonance (NMR) structure calculation. 
  • CYANA
    Allows for automated nuclear magnetic resonance (NMR) structure calculation. 

  • UNIO
    The UNIO program enables you to perform automated NMR data analysis and structure calculation for 3D protein structure determination. 

  • Xplor-NIH
    Xplor-NIH allows you to run NMR structure calculations with NOE, dihedral angle and paramagnetic restraints on the WeNMR grid infrastructure.

  • CcpNmr WMS
    Simplified job submission starting from CCPN data projects, with a unified interface for running either CYANA, UNIO, CS-ROSETTA, or ARIA. Calculations with multiple programs can be started from a single input selection.

Molecular Dynamics Simulation

  • AMBER
    Amber is a suite of programs that allow users to perform molecular dynamics (MD) simulations on biological systems. 

  • GROMACS
    GROMACS is a versitile package to perform molecular dynamics. GROMACS is able to work with proteins, lipids, nucleic acids and other molecules. 

Modelling

  • 3D-DART
    The 3D-DART server  provides a convenient means of generating custom 3D structural models of DNA with control over the local and global conformation. 

  • HADDOCK
    HADDOCK is an information-driven flexible docking approach for the modeling of biomolecular complexes. 

Various Software Tools

  • Format Converter
    The CcpNmr FormatConverter web interface was designed to facilitate conversions between any existing NMR data formats and types. 

  • SHIFT2X
    SHIFTX2 predicts both the backbone and side chain 1H, 13C and 15N chemical shifts for proteins using their structural (PDB) coordinates as input.

  • RCI
    The RCI webserver predicts protein flexibility by calculating the Random Coil Index from backbone chemical shifts (Cα, CO, Cβ, N, Hα, NH) and estimating values of model-free order parameters as well as per-residue RMSF of NMR and MD ensembles from the Random Coil Index. .

  • Antechamber
    The antechamber suite automates the process of developing a charge distribution and assigning atom types, and partially automates the process of developing parameters for the various combinations of atom types found in a given molecule. Antechamber can thus automatically generate AMBER input force field parameters for most organic molecules.

  • PREDITOR
    PREDITOR is a program for PREDIcting φ, ψ, χ1, and ω TORsion angles in proteins  from 13C, 15N and 1H chemical shifts and sequential homology. PREDITOR's accuracy in predicting φ and ψ is close to 90%.

  • RCI
    RCI webserver predicts protein flexibility by calculating the Random Coil Index from backbone chemical shifts (Cα, CO, Cβ, N, Hα, NH).

  • UPLABEL
    UPLABEL is an algorithm for finding optimal labeling patterns for the backbone assignment of proteins.

  • sedNMR
    sedNMR allows for simple calculation of the relevant parameters for a successfull Magic Angle Spinning (MAS) solid state NMR experiment. It is possible calculate the concentration gradient that is formed during MAS at different rates and the amount of sedimented protein for a given concentration via the eq.ns reported in (Bertini et al., PCCP, 14, ..., 2012). It is also possible to calculate the least concentration required to sediment a protein a the least MW that the protein should have to sediment.

 

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.

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