Software
This is a script-based processing programme which is used in combination with NMRDraw to visualise the data. It has been developed by scientists at the NIH and is free for academic users. This software is written by Bruker and is used on their NMR machines. It has a relatively straight forward GUI. Some people may still be using Bruker's old software, XWinNMR. Licences have to be paid for. TopSpin runs on a variety of operating systems. This is a commercial programme based on a GUI. Extensions can be written using Fortran. Azara is a suite of programmes to process and view NMR data. It is free for academic users. This is a new assignment programme and one of the best available. It is still being developed and has a very good mailing list. The preferred operating system is Linux (or MAC). It is mainly written in Python and users can write their own macros using the API. CCPNmr Analysis is part of the CCPN project which is funded by the UK Biotechnology and Biological Sciences Research Council. This is a very popular assignment program, but is apparently no longer being actively developed. It is written in Python and users can write their own extensions. Currently it is probably a better programme for making nice figures of your spectra than CCPNmr Analysis. It is free for academic users. Another widely used assignment programme which is still being actively developed and is free for academic users. This is a programme which was developed in the laboratory of Kurt Wüthrich. It is free for academic users. This NMR assignment programme has essentially been superceded by CCPNmr Analysis. This automatic backbone assignment programme uses chemical shifts from 3D assignment spectra and secondary structure prediction as its input. It can also assign the backbone using RDC data and a known structure of the protein. This programme will return the most probable sequence location for a short connected set of residues in a protein given 13Cα chemical shifts (δ(13Cα)) and data restricting the φ and ψ backbone angles. This new 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 algorithm assigns the backbone of a protein given the sequence and peak lists from standard 3D NMR spectra. This is a GUI based program for computer aided resonance assignment which was developed in the lab of Kurt Wüthrich. 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. 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 CCPNGrid webinterface - 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. 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 new 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 new 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. 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. 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, CNS, CYANA, HADDOCK and CS-ROSETTA. See here for a full list. MolMol was written specifically with NMR users in mind and is therefore good at dealing with ensembles. It is also able to display certain types of NMR restraints and violations and has many additional functions such as being able to calculate mean structures, RMSDs, show Ramachandran plots etc. Loading non-protein/peptide molecules can unfortunately cause problems and the manual can sometimes seem rather cryptic which makes it hard to get the most out of the programme unless you have an advanced user to hand who can help you. MolMol can be operated via a GUI, but is also possible to write scripts to carry out a series of commands. Rasmol is quite a nice programme for looking at molecules quickly. Unfortunatley, the normal version is not able to deal with ensembles very well (or possibly at all). It is also not brilliant for generating high quality graphics for publication. However, it is developed quite a bit in the mean time and the newer versions might be more useful to NMR users. PyMol is a python-based molecular viewer which is able to generate beautiful pictures with excellent light effects. It is thus good for making publication-quality images. I know very little about this, but everyone who uses it raves about it. This is a version of VMD which the NIH NMR groups have adapted to work with XPLOR-NIH. It is thus able to show restraints and violations and other such things which are useful for NMR spectroscopists. This is quite a nice programme for looking at proteins. It has various exciting functions such as being able to mutate a sidechain, change torsion angles, add hydrogens, very easily measure inter-atomic distances and a magic-fit which will fit non-identical proteins. But it has no NMR-specific functions. This is a new project from CCP4. It is fairly intuitive to use and has good online tutorials. It can deal with NMR ensembles, with ligands and with crystal lattices and is thus fairly versatile. But as it is written by crystallographers it does not have any facilities for looking at NMR restraints and suchlike. This is actually a programme for modelling crystal structures, but it has quite nice graphics. It doesn't handle hydrogen atoms very well, so it isn't ideal for NMR structures. However, it is possible to look at crystal strutures with the symmetry molecules included - excellent for investigating crystal contact areas! This is an extremely useful webserver which will run your structure through various programs. It will check for violations, calculate the RMSD (overall and ordered regions only) and run it though a variety of structure validation programs such as the Protein Data Bank Validation Suite, Procheck, ProsaII, MolProbity and Verify3D. Definitely use this site during your structure calculation stage and before submitting a structure to the PDB. This programme will analyse your restraints for their information content. It will show up restraints which have a large effect on the structure and/or which are not supported very well by other restraints. You should probably be very sure of such restraints before leaving them in your calculation. It uses up a lot of CPU time and the calculation of Iave (how well supported is each restraint by others) is best run on a cluster. This is a new programme for NMR protein structure validation which can be run on the iCING server. This is quite a large software package which is actually meant for modelling, but it includes a range of structure validation tools. Although the programme can be run locally, it is probably best to use the webserver. Be aware that some of the databases used for these may not necessarily be very up-to-date. You may get worse Z-values than from some of the PSVS programs. The algorithm to investigate atomic clashes also differs from those used by the PDB and MolProbity. Talos uses a database of chemical shifts of proteins for which high resolution crystal structures are available. By matching amino acid type and chemical shifts (N, HN, Cα, Cβ, CO) to triplets of amino acids from the database, it predicts the average φ and ψ angles for your protein. Sparta will predict chemical shifts based on a 3D structure. David Wishart's group has done a lot of work on chemical shifts of proteins over the years and have a number of web servers which will do varying things including predicting chemical shifts from the structure or sequence of a protein, predicting secondary structure from chemical shifts, or automatic assignment and structure calculation using an HNCACB peak list as input. This GUI based programme allows you analyse residual dipolar coupling data and determine order tensors as well as back-calculate couplings from a given order tensor and structure. Additional algorithms are included for things such as error analysis or the simulation of the effects of dynamic averaging processes. Another GUI based programme for anaylsing residual dipolar couplings as well as chemical shift anisotropy arising from residual alignment of a protein. This programme allows you to predict the alignment tensor (and thus the RDCs) of a protein from its structure. This can be done on the basis of both steric and electrostatic alignment. The very first programme developed to analyse relaxation data within the Libari-Szabo model free formalism. The associated CPMGFit can be used to fit relaxation dispersion data. A GUI based programme for analysing relaxation data within the Libari-Szabo model free formalism. This programme for the analysis of relaxation data within the Libari-Szabo model free formalism includes novel model selection methods. It also includes spectral density mapping. DASHA can be used for the analysis of relaxation data within the Libari-Szabo model free formalism as well as spectral density mapping and the analysis of relaxation dispersion data. This is a software package which allows you to simulate solid-state NMR experiments. This software can be used to simulate both solid-state and solution-state NMR experiments.
Various Labs have developed quite a number of different software packages over the years and no doubt more will be added. It would not be possible to list every single programme on this web page, so here is a link to many of these labs' software pages.
