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 for 3D protein structure determination. It includes data analysis algorithms for all parts of an NMR structure determination process ranging from backbone and side-chain assignment to NOE assignment and structure calculation.

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 for 3D protein structure determination. It includes data analysis algorithms for all parts of an NMR structure determination process ranging from backbone and side-chain assignment to NOE assignment and structure calculation.

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

Analysis

• TALOS+
  is, as the original program TALOS, 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
  The WeNMR MaxOcc webportal provides an user friendly graphical user interface for making 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 (Common Interface for NMR structure Generation).  

Molecular Dynamics Simulation

• AMBER
  Amber (acronym to Assisted Model Building with Energy Refinement) 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, i.e simulate the Newtonian equations of motion for systems with hundreds to millions of particles. GROMACS is able to work with many biochemical molecules like proteins, lipids and nucleic acids. The WeNMR GROMACS webportal combines the versitility of this molecular dynamics package with the calculation power of the eNMR grid. This will enable you to perform many simulations from the comfort of your internet browser anywhere in the world. The server is furthermore aimed to provide a user friendly and efficient MD experience by performing many preperation and optimization steps automatically.

Modelling

• HADDOCK
  HADDOCK (High Ambiguity Driven protein-protein DOCKing) is an information-driven flexible docking approach for the modeling of biomolecular complexes. 

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

Various Software Tools

• Format Converter
  The CcpNmr FormatConverter web interface was designed to facilitate conversions between any existing NMR data formats and types. The underlying code is based on the existing CcpNmr FormatConverter code.

• 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.