DATABASES AND LINKS


S
PECTROMETER 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, Israel) and Eidgenössische Technische Hochschule Zürich (ETH Zurich, Switzerland)


D
ATA PROCESSING AND ANALYSIS

  • matNMR
    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
    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
    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
    A multi-purpose NMR program designed for the processing, the display and the analysis of 1D, 2D & 3D NMR data-sets. M. A. Delsuc, CBS, France.
  • 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.
  • Sparky
    Graphical NMR assignment program for proteins and nucleic acids. Runs under Windows, Linux, or Unix.
  • Azara
    A suite of programs to process and view NMR data. Courtesy of 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.
  • CARA
    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
    A program for robust automatic backbone assignment of 13C/15N labeled proteins. Courtesy of Markus Zweckstetter, Max Planck Institute for Biophysical Chemistry, Germany.
  • HiRes
    High Resolution Spectroscopy (HiRes), is a free Windows software program to provide comprehensive analysis of large NMR spectroscopic data sets. It 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.


S
IMULATION AND ANALYSIS

  • 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.
  • FIRM
    Full Iterative Relaxation Matrix program is an 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, USA.
  • GAMMA
    A library written for simulation of Nuclear Magnetic Resonance experiments. 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.
  • 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.
  • MORASS
    Multiple Overhauser Relaxation AnalysiS and Simulation uses a full hybrid matrix eigenvalue/eigenvector solution to the Bloch equations to derive cross-relaxation rates and interproton distances. It analyses 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.
  • QSim
    A rogram for simulation of liquid state NMR experiments. It 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 visualisation 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) is 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.
  • WINDNMR-Pro
    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.


N
MR 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 of Torsten Herrmann.
  • TALOS
    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).
  • CYANA
    A program for automated structure calculation of biological macromolecules on the basis of conformational constraints from NMR. The combination of automated NOESY cross peak assignment, structure calculation with a fast torsion angle dynamics algorithm, and the ease-of-use of CYANA provide for unprecedented efficiency in NMR protein structure determination.
  • CNS
    Crystallography & NMR System (CNS) is the result of an international collaborative effort among several research groups. The program has been designed to provide a flexible multi-level hierachical approach for the most commonly used algorithms in macromolecular structure determination. Highlights include heavy atom searching, experimental phasing (including MAD and MIR), density modification, crystallographic refinement with maximum likelihood targets, and NMR structure calculation using NOEs, J-coupling, chemical shift, and dipolar coupling data.
  • XPLOR-NIH
    A structure determination program which builds on the X-PLOR program, including additional tools developed at the NIH.


M
ISCELLANEOUS


C
OMMERCIAL PRODUCTS

  • HaveItAllTM NMR
    This 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. Bio-Rad Laboratories, Inc., Informatics Division.
  • 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 Inc.
    • Chenomx Profiler
      A broad range of tools to assist in identifying and quantifying compound concentrations based on data in an NMR spectrum. Using a compound library of over 260 unique spectral signatures together with sophisticated computer-assisted fitting routines, you can accomplish in minutes what would have taken hours or days using manual analysis methods.
    • Chenomx Compound Builder
      Developed to address a recurring customer request: the capability to add custom compounds to a Compound Library. Allows a user to create a signature that models the compound of interest. This capability lets users create signatures for compounds that are not present in the standard Chenomx Compound Library, and subsequently use those proprietary compounds in an analysis within Profiler.
    • Chenomx Spin Simulator
      A simple yet powerful tool for creating simulations of NMR spectra, based on user-defined spin systems, coupling relationships and reference spectra. You can use these simulations as starting points for creating your own compound signatures based on fundamentals of NMR theory.
    • Chenomx Library Manager
      Allows you to create and manage Compound Sets for use in Profiler. Compound Sets can contain any compound signatures in your library, including those from the Chenomx library as well as those that you create with Compound Builder. You can tailor a Compound Set to a specific project. For example, in a research project, you may only be interested in examining the concentrations of five particular compounds for a drug study; you can use Library Manager to create a Compound Set including only those compounds.
    • Chenomx Processor
      Allows a variety of native spectrum formats, such as Varian, Bruker, and JCAMP to be converted into the Chenomx file format.
  • magritek's PROSPA
    NMR Processing Package for Windows especially suitable for NMR Imaging and Research applications.
  • 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
  • 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.
  • 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 experimental chemical shifts and coupling constants. ACD/CNMR brings you the fastest and most accurate 13C NMR prediction engine available based on the analysis and correlation of observed chemical shifts and coupling constants. ACD/Labs also offers NMR prediction modules for 15N, 19F, and 31P.
  • Woody Conover's (Acorn) SAM, NUTS, and Virtual Spectrometer.
  • Felix NMR Inc. - FELIX
    Felix is the industry standard software program for off-line data processing, spectral visualization and analysis of high resolution, one- to four-dimensional, homonuclear and heteronuclear NMR data. It is available as a workstation product that runs on Linux or SGI and as a desktop product for Windows PCs.
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