NMR Information Server: Software

SPECTROMETER CONTROL SOFTWARE

DAMARIS (Darmstadt Magnetic Resonance Instrument Software) - develops a framework for NMR spectrometer controls, open source, maintained by Achim Gädke, courtesy of NMR groups at TU Darmstadt: AG Nestle and AG Fujara.
SpecMan - Spectrometer Manager - the shell for pulse EPR experiments, also applicable to pulse NMR experiments. Courtesy of Boris Epel, Igor Gromov and Stefan Stoll, with Daniella Goldfarb and Arthur Schweiger, Weizmann Institute of Science (Rehovot) and Swiss Federal Institute of Technology (Zurich).
SpinCore Matlab GUI Interface to RadioProcessor - program created for the MATLAB environment that allows quick and easy interaction with the SpinCore RadioProcessor boards.

DATA PROCESSING AND ANALYSIS

MddNMR - a program for processing of non-uniformly sampled (NUS) multidimensional NMR spectra. The package contains also a routine to produce NUS schedule that can be used to setup N-dimensional NUS NMR experiments. Potentially any pulse sequence can be run in the NUS mode. In the NUS acquisition, only a fraction of full (conventional) data set is recorded. MddNMR works by replenishing missing data points in the full matrix followed by regular FT processing of the complete data.
TARQUIN - analysis tool for automatically determining the quantities of molecules present in NMR spectroscopic data. The intended purpose of TARQUIN is to aid the characterisation of pathologies, in particular brain tumours, both non-invasively with in-vivo 1H MRS and ex-vivo with 1H HR-MAS.
rNMR - open source software for NMR data analysis. rNMR simplifies repetitive resonance assignments and quantification tasks common in metabolomics, titrations, and small molecule analyses. Versions of rNMR are available for Windows, Macintosh, Linux, and Unix (courtesy of the University of Wisconsin-Madison).
matNMR - matNMR is a highly flexible processing toolbox for NMR and EPR spectra under MATLAB (all platforms). It can read in binary FID's from most commercial spectrometers, process any 1D or 2D spectrum and uses all graphical capabilities that MATLAB has to offer. The program is fully GUI and at all times allows the user to profit from MATLAB's numerical powers (courtesy of Jacco van Beek, ETH Zurich).
NMRPipe - NMRPipe provides comprehensive facilities for Fourier processing of spectra in one to four dimensions, as well as a variety of facilities for spectral display and analysis. It is currently used in over 300 academic and commercial laboratories (courtesy of the Ad Bax group).
MestRe-C - from Spain - MestRe-C 2.0 is a program designed to process and plot 1D NMR spectra on PC’s running Windows 95/98/NT 4.0. It imports files from most spectrometers and includes a number of useful tools (courtesy F. Javier Sardina, Universidad de Santiago de Compostela, SPAIN).
RMN - a Nuclear Magnetic Resonance (NMR) data processing program for the Macintosh. Dr.Philip J. Grandinetti
Gifa - "The Gifa program is a multi-purpose NMR program. It is designed for the processing, the display and the analysis of 1D, 2D & 3D NMR data-sets." M.A.Delsuc, CBS, France.
NMR Desk - 1D and 2D data processing and simulation (MS Windows).
CROSREL - "a program for the analysis of ROESY and NOESY NMR data" - Bas R. Leeflang, Utrecht, The Netherlands.
MARDIGRAS"(Matrix Analysis of Relaxation for DIscerning the Geometry of an Aqueous Structure) is a FORTRAN program for calculating proton-proton distances from cross-peak intensities measured from a 2D NOE experiment."- UCSF, USA.
PRONTO - FAQ Pronto: The PROtein Nmr TOol - Mogens Kjaer, Carlsberg Laboratory, Denmark. Source.
ANSIG Assignment of NMR Spectra by Interactive Graphics (written in Fortran 77 for Silicon Graphics machines). ANSIG is a program for viewing and assigning 2D, 3D and 4D NMR spectra (both homonuclear and heteronuclear) of biological macromolecules, mainly proteins. The input data for the program are frequency-domain spectrum matrices, together with the sequence of the protein. All processing (FT, LP, MEM, baseline correction, and the like) of the spectral matrices must have been done before ANSIG can be used to view the spectra (Courtesy of Per Kraulis). ANSIG has been ported to Windows/OpenGL - see the home page at http://www.csb.ki.se/nmr/AFW.html
Sparky - Graphical NMR assignment program for proteins and nucleic acids. Runs under Windows, Linux, or Unix.
Azara - Azara is a suite of programs to process and view NMR data. Courtesy Wayne Boucher.
iNMR (evolution of SwaN-MR) : "An NMR processing software for the Macintosh. It reads 1D, 2D, 3D and 4D spectra coming from many spectrometers and its feature list is comparable to those of commercial packages". Giuseppe Balacco.
V - an interactive software system for MR signal processing. Source
CARA - CARA is a program for computer-aided resonance assignment of multidimensional NMR spectra of macromolecules. Dedicated tools along with a well organized database allow for efficient assignment. Custom applications can be developed with scripts. All major platforms are supported.
MARS is a program for robust automatic backbone assignment of ¹³C/¹⁵N labeled proteins (curtesy Markus Zweckstetter, Max Planck Institute for Biophysical Chemistry, Germany).
BACUS - Software for the analysis of NMR data for protein structure computation. A Bayesian protocol for the identification of protein NOESY spectra via unassigned spin systems. Free download for Academic (Non-Profit) Institutions. Registration is required. Courtesy of Miguel Llinás group, Carnegie Mellon University, Chemistry.
HiRes - High Resolution Spectroscopy (HiRes), is a free Windows software program to provide comprehensive analysis of large NMR spectroscopic data sets. HiRes combines standard spectral processing routines, data correction functions, techniques for reducing information complexity of multi-spectral dataset such as Principal Component Analysis (PCA), and tools for Pattern Recognition, such as Non-Negative Matrix Factorization (NMF), which extracts a set of spectral patterns with direct physical interpretation that can be used for identifying meaningful biochemical effects. These spectral patterns are also correlated with auxiliary information from the samples, such as biological end-points, drug toxicity or disease diagnosis. Courtesy of Columbia University, New York, USA.
3DiCSI - 3D Interactive Chemical Shift Imaging (3DiCSI) is an interactive, user-friendly, and comprehensive software program for multi-dimensional CSI data visualization, spectral processing/analysis, spectral localization, and quantification. It currently runs on Windows platform and is provided as a software free for research. Courtesy of Qi Zhao, Columbia University.

SIMULATION AND ANALYSIS

AMBER - a general purpose molecular dynamics and simulation package, with many features relevant to NMR structure determination. These include time-averaged restraints, diamagnetic and paramagnetic chemical shift restraints, and "direct" refinements against NOESY volume data.
CORMA - (COmplete Relaxation Matrix Analysis) is a FORTRAN program for calculating the dipole-dipole relaxation matrix for a system of protons and converting that to intensities expected for a 2DNOE experiment." - UCSF, USA.
DSYMPC"NMR SIMULATION AND ITERATION TOOLS FOR PCs" - G. Hdgele at al., Duesseldorf, Germany.
FIRM - Full Iterative Relaxation Matrix program. "Interactive program (fortran) for calculating NOEs of a structural model using the relaxation matrix approach. Distances, corrected for the effects of spin diffusion, can be back-calculated from experimetal NOEs using a hybrid relaxation matrix. Includes features for simulating internal motions". (S. Edmondson, University of Alabama in Huntsville).
GAMMA - "a library written for simulation of Nuclear Magnetic Resonance experiments" - ref: S.A. Smith, T.O. Levante, B.H. Meier and R.R. Ernst (ETH, Switzerland); Computer Simulations in Magnetic Resonance: An Object-Oriented Programming Approach, Journal of Magnetic Resonance, November 1993, Series A. (ftp link to ETH).
Insensitive - (Incredible Nuclear Spin EvolutioN SImulation Tool Intended for Visual Education) This free BETA software simulates the NMR experiment by visualizing three models (vector model, product operator formalism, and the density matrix approach). The user can interact with every step of the spectrum from the first pulse to the phase correction of the acquired spectrum after Fourier transformation. Klaus Boldt, University of Hamburg.
MathNMR - Mathematica package for NMR spin and spatial tensor manipulations. Arbitrary spin systems, commutators, projection operators, rotations, Redfield matrix elements, matrix decomposition into basis operators, change of basis, coherence filtering, and the manipulation of Hamiltonians. The package is available for free. Alexej Jerschow, NYU.
MEX and CIFIT - Alex Bain: "For simulation of exchanged-broadened lineshapes for uncoupled spin systems (MEX) and "to analyse selective inversion experiments (Hoffman-Forsen) for slow chemical exchange (CIFIT).
MORASS - Multiple Overhauser Relaxation AnalysiS and Simulation. "MORASS uses a full hybrid matrix eigenvalue/eigenvector solution to the Bloch equations to derive cross-relaxation rates and interproton distances. MORASS analyzes 2D NMR NOESY data from oligonucleotides and proteins to evaluate cross-relaxation rates from which interproton distances are obtained" - R.P. Meadows, C.B. Post, and D.G. Gorenstein, Purdue Univ. USA.
NUMARIT- "A spin simulation/iteration package for the X32", by Kirk Marat.
PC Software: APT, DECAY, DEPT, FIDUNK, FTNMR Simulator, HETJ-2D, HOMOJ-2D, IRREADER, NMRSM, UNKINP, XHCORR from Dr. Harold M. Bell, Department of Chemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
PERCH - (PEak reseaRCH) - an integrated NMR-software package for research, analytics and education. The spectral analysis and simulation up to 10 spins is based on the program MLDC (Modified LAOCOON with Dipolar Couplings)" - PERCH Project, Univ. of Kuopio, FINLAND.
PJNMR - PJNMR allows visualization and simulation of up to a three spin heteronuclear or homonuclear system for pulse sequence creation.
QSim - program for simulation of liquid state NMR experiments. QSim has a graphical user interface, and pulse sequences are set up graphically. Pulse sequence elements that can be simulated include gradients, shaped pulses and decoupling sequences. Spin systems with any NMR-active nuclei can be simulated. Relaxation is included in all parts of simulations. First order chemical exchange may be included in simulations. Simulations are performed using quantum mechanical or classical mechanics. Processing may be performed in the program and 1D and 2D spectra plotted. Courtesy of Magnus Helgstrand, Dept. of Biophysical Chemistry, Lund University, Sweden
SIMMOL - Software for specification and 3D visualization of anisotropic interaction tensors from pdb-structure of peptides and proteins. The software allows straigthforward establishment of the orientations and magnitudes of anisotropic tensors for numerical simulations of peptide/protein solid-state NMR spectra using SIMPSON - Mads Bak, Robert Schultz, Thomas Vosegaard, and Niels Chr. Nielsen
SIMPSON - (SIMulation Package for SOlid-state Nmr spectroscopy) - A free solid-state NMR simulation program with emphasis on ease of use. Multiple pulses, spins, and dimensions. Flexible Tcl input files. Extended documentation for various experiments - Mads Bak, Jimmy T. Rasmussen, and Niels Chr. Nielsen, Lab. Biomol. NMR, Aarhus, Denmark.
Spinach - Spinach is a fast (polynomial complexity scaling for liquid state NMR) open-source spin dynamics simulation library that supports NMR, EPR, DNP, MAS, Optimal Control, PHIP, singlet state NMR and other forms of Magnetic Resonance spectroscopy. Spinach history and capabilities are summarized in the 2013 EPR Newsletter.
SPINDROPS - The free SpinDrops app provides a highly interactive and visual approach to simulate the spin dynamics of magnetic resonance experiments based on the DROPS representation. The app uses the novel DROPS representation to depict arbitrary spin states in an intuitive and compact way.
SPINEVOLUTION - is a flexible general purpose NMR simulation package suitable for simulation of a wide range of NMR experiments from CW liquid state NMR to solid state rotor-synchronized MAS experiments, PFG experiments and optimization of shaped pulses. SPINEVOLUTION offers a simple non-algorithmic definition of pulse sequences which authors called "canonical representation". Courtesy of Mikhail Veshtort, MIT, Massachusetts, USA.
WINDNMR-Pro (DNMR71.EXE) - is a Windows program for simulating high resolution NMR spectra. The 16-bit version of WINDNMR was published by the Journal of Chemical Education - Software. The program will run on all versions of Windows (95, 98, NT, ME, 2000, XP, Professor Hans J. Reich, Department of Chemistry, University of Wisconsin, Madison, USA.

NMR STRUCTURE CALCULATION AND REFINEMENT

Standalone ATNOS/CANDID program - the standalone ATNOS/CANDID program bundles together the two algorithms ATNOS for automated NOESY peak picking and CANDID for automated NOE assignment and whereby provides a powerful platform for objective and efficient de novo 3D protein structure determination by NMR. Courtesy Torsten Herrmann.
TALOS- TALOS is a database system for empirical prediction of phi and psi backbone torsion angles using a combination of five kinds (HA, CA, CB, CO, N) of chemical shift assignments for a given protein sequence. (courtesy of the Ad Bax Group).
DYANAis a new program for NMR structure calculation that provides all functionality of its predecessor, DIANA, and many new features - Peter Güntert, guentert@mol.biol.ethz.ch
DINOSAUR- "A set of programs for structure refinement using direct NOE restraints" - Alexandre Bonvin, while with the NMR Group at Utrecht University, the Netherlands.
IRMA2 "The IRMA procedure calculates distances from experimental NOE spectra with the use of the full relaxation matrix approach". the NMR Group at Utrecht University, the Netherlands.

DYNAMICS

DASHA - Model-Free Analysis of Protein Dynamics from Heteronuclear NMR Relaxation Data, and DIFFC: Hydrodynamic calculations for proteins with known spatial structure - both developed at the Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, RAS, Moscow, Russia; General advising - Prof. Alexander S. Arseniev.

ModelFree - a program for optimizing "Lipari-Szabo model free" parameters to heteronuclear relaxation data. Written by Arthur G. Palmer, III.

NESSY - an open source software to analyse NMR relaxation dispersion data of either CPMG or R1p (R1rho) dispersion experiments. The graphical interface enables simple management of large experimental data sets and simple and automated analysis. NESSY autamatically calculates effective transverse relaxation rate (R2eff) and performs model selection between different relaxation dispersion models. Written by Michael Bieri.

relax - a software package designed for the study of molecular dynamics through the analysis of experimental NMR data. Organic molecules, proteins, RNA, DNA, sugars, and other biomolecules are all supported. It was originally written for the model-free analysis of protein dynamics, though its scope has been significantly expanded.

Tensor - the latest version of the program for treating solution state 15N relaxation for the study of molecular dynamics. Originally devised for the study of rotational diffusion of macromolecules the program now allows for the determination of internal mobility parameters using the model-free approach from Lipari and Szabo, either in the case of isotropic or anisotropic overall molecular diffusion.

VISUALIZATION

Pencil Home Page - "Pencil is a visualization package for NMR and MRI experiments" - Jonathan Callahan, Univ. of Washington, USA.

IMAGE VIEWING, IMAGE RECONSTRUCTION

MRIcro - Free medical image viewer for Windows; it can display and convert Analyze, DICOM, ECAT, NEMA, GE Signa & LX, Interfile, Picker CT, Siemens Magnetom, and raw data format images - Chris Rorden.
HF- NMR Image Reconstruction from Partial K-Space Data; in Visual C++, for Windows 95. P.F.Tokarczuk@cranfield.ac.uk (Dr. Pawel F. Tokarczuk).

MISC.

Jean-Marc Nuzillard NMR software homepage at http://www.univ-reims.fr/LSD/JmnSoft
MagRes,Web-based magnet reservation, courtesy University of Indiana.
NMRPal - NMR calculator and data tables for PalmOS (by Blaise Frederick).
PalmNMR - Lists frequencies, gyromagnetic ratios, natl. abundances, receptivities, magnetic and quadrupolar moments, and reference compounds of most NMR active nuclei (by Alexej Jerschow).
Pocket NMRinfo - PocketPC database of NMR properties, chemical shifts, etc.
Peter Lundberg's Compilation of Educational NMR Software; (courtesy of Graham Barlow).
Rudi Nunlist's Software Archive
Software available from Lewis Kay's group
Software available from Malcolm Levitt's group
Software available fromMontelione's group
Software available from Natl. Magn. Reson. Facility at Madison
Software available from Biomolecular NMR Facility at UAH
Software available from University of Pennsylvania
Software available from Biomedical Magnetic Resonance Laboratory, Univ. of Illinois, Urbana-Champain

COMMERCIAL PRODUCTS

Accelrys' FELIX - NMR data processing, analysis and assignment program.

ACD/Labs’ NMR Prediction Software -- ACD/HNMR enables you to calculate the proton NMR spectrum for any organic structure to a high accuracy. Prediction is based on an internal data file with over 1,384,000 experimental chemical shifts and 449,000 coupling constants. ACD/CNMR brings you the fastest and most accurate 13C NMR prediction engine available based on the analysis and correlation of over 2,017,000 observed chemical shifts and 81,000 coupling constants. ACD/Labs also offers NMR prediction modules for 15N, 19F, and 31P.

Bio-Rad Laboratories, Inc., Informatics Division's - HaveItAll^TM NMR. This new product offers spectroscopists and other analytical chemists a reliable source of NMR data of over 140,000 13C and 12,000 1H spectra they can use as a reference in the first, fully integrated environment for NMR. The HaveItAll NMR database works within and includes Bio-Rad's new KnowItAllT Analytical System. With the combined power of the high-quality HaveItAll NMR data and the KnowItAll environment, researchers can have it all and know it all in one place-make predictions, search, access reference spectra, build databases with assignments (with KnowItAll's Database Building Option and AssignIt(TM) Option), and even cross-reference NMR data with other analytical techniques, such as IR, UV/Vis, GC, MS, Near IR, and Raman, and generate high-quality reports.

Chenomx Inc. - Chenomx NMR Suite: Specialized NMR spectra analysis platform for metabolic profiling. By integrating a broad range of tools into the platform, Chenomx NMR Suite delivers unparalleled power and ease of use to assist you with NMR spectra analysis and interpretation.
- Chenomx Profiler – Assists you in identifying and quantifying metabolic compounds within bio-fluid samples. Using a Compound Library of over 200 unique spectral signatures together with computer-assisted routines, a user can accomplish in minutes what would have taken hours or days using manual analysis methods;
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Seeing is believing – please visit http://www.chenomx.com to download and try the evaluation version of Chenomx NMR Suite 4.0.

magritek's PROSPA - NMR Processing Package for Windows especially suitable for NMR Imaging and Research applications. Version 1.9 has just been released. Developed by Dr. Craig Eccles. New features coming soon include 2D Laplace inversion and enhanced 3D visualisation. Can process and display 1D, 2D and 3D data sets acquired with a number of different NMR spectrometers. http://www.magritek.com/prospa

Mestrelab Research S.L - Feliciano Barrera 9B – Bajo, 15706 Santiago de Compostela, Spain. +34 (881) 976 775, US Office: (858)736-4563, e-mail: sales@mestrelab.com, Internet: www.mestrelab.com. Mestrelab Research develops MestreNova (Mnova) software for processing, analysis, reporting and managing 1D and 2D NMR and LC/GC/MS data on desktop computers (Window, Mac or Linux). The Mnova software package currently includes the following plugins:
- Mnova NMR: For processing and analysis of 1D and 2D NMR from all vendor formats. Features include global spectral deconvolution (GSD) for more reliable peak picking and integration in H-1 spectra, 1D and 2D correlated peak assignments, efficient analysis of arrayed spectra, and scripting capabilities for automation.
- Mnova NMRPredict Desktop: For prediction of H-1, C-13, N-15, O-17, F-19, Si-29, P-31 chemical shift and H-1 coupling constants.
- Mnova MS: For processing and analysis of LC/MS and GC/MS data from most vendor formats. Features include automatic molecule match by comparison of molecule ion and isotope patterns for verifying proposed structures.
- Mnova DB: For creating your own databases (MySQL or Oracle based), and managing your molecular structures and analytical data (including the raw data, processed data, and analysis results of NMR and LC/GC/MS).
- Mnova Verify: For automated structure verification using H-1, HSQC NMR and/or LC-MS data and ranking of structural candidates in the light of analytical data.

ScienceSoft's NMRanalyst: Computerized analysis of phase sensitive 1D through 3D NMR FIDs and spectra. Generates accurate spin system descriptions including signal integrals and coupling constants. Sold by Varian, Inc. as "Full Reduction of Entire Datasets", FRED(tm).

Spectrum Research - CASE - As a part of a new generation of "Computer Assisted Structure Elucidation (CASE)" programs we have developed an expert system of programs called SpecMan and NMR-SAMS, which take into account the spectroscopist's experience and knowledge into the process of spectrum interpretation and structure generation. They provide the spectroscopist the opportunity to work more efficiently and rapidly.

Umatek's ADVASP - The ADVASP spectra analysis software is designed especially for total customer satisfaction in analyzing IR, MASS and NMR spectra. The main idea in creation of this program is to make user interface as easy as possible from one side and as functional as it is required by professionals.

Woody Conover's (Acorn) SAM, NUTS, and Virtual Spectrometer.

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