NMR Services

Processing

• MDD NMR
  This service allows to process a non-uniformly sampled (NUS) nD spectrum using Multi-Dimensional Decomposition program. 

Assignment

• Auto Assig
  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. 

• 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.

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.