Structure Calculation

This is a popular NMR structure calculation programme. Many groups have written new modules for this programme and any developed by the NMR groups at NIH are automatically incorporated. Free for academic users. Also available via the WeNMR Webportal.

This is based on XPLOR and many of the input styles are the same as for XPLOR / XPLOR-NIH. Free for academic users.

This is a programme which will automacially assign your NOE spectra and calculate the structure using CNS. At one point the convergence was not as good as for CYANA, but in the mean time with the incorporation of new modules this has probably improved. SolARIA, an old version of ARIA suitable for calculating structures from solid-state NMR data is being incorporated. ARIA uses the CCPN Data Model and it is thus possible to read your CCPNmr Analysis project directly into ARIA and set up the calculation. You can also use ARIA via the CCPNGridwebinterface – useful if you don’t have your own cluster to hand.

CYANA is another programme which will automatically assign your NOE spectra and calculate the structure. The structure is calculated using DYANA which is based purely on torsion angle dynamics (rather than using cartesian co-ordinates as XPLOR and CNS do). This makes it a computationally very fast and efficient program. CYANA has quite good convergence properties. The main downside is the lack of a good manual – it can thus end up being used as a bit of a black box or not to its full potential. Also available via the WeNMR Webportal.

This program not only automatically assigns your NOE spectra along with calculating your structure, it also automatatically removes artifacts from your spectra and can backcalculate NOE spectra.

This program subsumes the previous MATCH/ATNOS/CANDID algorithms. It uses APSY and NOESY data as its input and is then able to carry out backbone and side-chain assignment as well as NOE assignment and structure calculation.

This is a webserver which uses chemical shift and (assigned) NOEs to calculate the structure. During the early stages of the calcualtion homology modeling is used to quickly generate a good starting structure.

A webserver which will calculate a 3D structure using only chemical shifts as input.

This software is a new version of ROSETTA, a molecular modelling software package. It calculates structures using only chemical shifts and the protein sequence as input. Also available via the WeNMR Webportal.

A method of determining protein structures using chemical shifts.

This is not strictly structure calculation software, but docking software (High Amgiguity Driven biomolecular DOCKing). It can be used for docking protein-protein, protein-DNA, protein-RNA, protein-oligosaccharide or protein-ligand complexes. As its input, it is able to use a large number of different NMR-based parameters as well as other biophysical and biochemical data such as SAXS or cryo-EM data or mutagenesis data. The software can be run locally or using the HADDOCK web server. Also available via the WeNMR Webportal.

Again, this is not strictly structure calculation software, but it is a useful tool when studying denatured or intrinsicually disordered proteins (IDPs). The software generates ensembles of molecules depending on the primary sequence of a protein, with the possibility of introducing additional local or long-range conformational propensities at an amino acid-specific level. In this way, the programme can be used to generate a broad ensemble of conformers representing the flexibility of an IDP of interest. The software can also calculate expected values of experimental parameters such as dipolar and scalar couplings, paramagnetic relaxation enhancements, chemical shifts or small angle scattering. In this way, it is useful for comparing experimental data with those expected from a fully disordered protein in order to detect deviation from ‘random coil’ behaviour.

This is an initiative funded by the European Union which enables users to make use of Grid technology to use NMR software. Several software packages are already available including XPLOR-NIH, CYANA, HADDOCK, CS-ROSETTA and CING. See here for a full list.