University of Wisconsin–Madison

Software

NMRFAM is active in the development of software tools that facilitate investigations by NMR. Advanced computational analysis algorithm research, new methods integration, user interface development, and instrument automation are combined to increase the accessibility, accuracy and efficiency of the range of methodologies employed. The software packages shown below are developed or supported at NMRFAM, and are available for download or remote use on our servers and spectrometers.

software overview chart

NMRFAM Webservers

[Go to the NMRFAM Webservers]

NMRFAM Software Tools

[Go to the universal NMRFAM Software download page]

ADAPT-NMR Assignment-directed Data collection Algorithm utilizing a Probabilistic Toolkit in NMR: a fully automated method for integration of optimized protein NMR data collection, chemical shift assignment, and secondary structure determination. PUBLICATION
ADAPT-NMR Enhancer
Software for visualization and analysis of tilted plane spectra derived from ADAPT-NMR. PUBLICATION
ALATIS
ALATIS (Atom Label Assignment Tool using InChi String) is an adaptation of InChI, which operates fully within the InChI convention to provide unique and reproducible molecule and all atom identifiers. PUBLICATION.
ARECA
ARECA (Assessment of the REliability of Chemical shift Assignments): A probabilistic validation of protein NMR chemical shift assignments against NOESY data. PUBLICATION
GISSMO
GISSMO (Guided Ideographic Spin System Model Optimization) is a methodology and software for efficient interactive optimization of spin parameters against experimental 1D-1H NMR spectra of small molecules. PUBLICATION.
HIFI-NMR
High-resolution Iterative Frequency Identification for NMR: an adaptive approach for rapid and automated collection of NMR data. PUBLICATION
LACS Linear Analysis of Chemical Shifts: a method for detection and automated correction of potential referencing problems and detection of inconsistent assignments – now included in PINE! PUBLICATION
Newton Spectral analysis of multidimensional NMR data useful for complex mixtures. Newton implements a Fast Maximum Likelihood Reconstruction (FMLR) of NMR spectra from spectral deconvolution of raw data that constructs the simplest time-domain model whose fourier processed spectrum most closely matches the spectrum of the identically processed FID. PUBLICATION
NMRbot High throughput data acquisition for Bruker NMR spectrometers running Topspin >2.0, fitted with ATM and SampleJet hardware accessories. PUBLICATION
NMRFAM-SPARKY SPARKY supports user-defined enhancements, and we have used these to develop new tools in support of our packages for automated protein assignment and structure determination. The added features support (1) interfacing with servers offering new technologies, (2) tools for data visualization and verification, and (3) new protocols for maximizing the efficiency of NMR data analysis. PUBLICATION
NMR Structure Tools
A PyMol add-on with tools for NMR structure ensemble analysis such as pairwise alignment, structure restraint validation and hydrogen-bond detection.
PACSY Protein structure And Chemical Shift NMR spectroscopY: a relational database management system that integrates information from the Protein Data Bank (PDB), the Biological Magnetic Resonance Data Bank (BMRB), and the Structural Classification of Proteins (SCOP) database. PUBLICATION
PECAN Protein Energetic Conformational Analysis from NMR chemical shifts: probabilistic secondary structure predictions from chemical shift– now included in PINE! PUBLICATION
PINE Probilistic Interaction Network of Evidence: a probabilistic algorithm for automated backbone and sidechain assignments, with detection and correction of referencing and secondary structure determination from input protein sequence and NMR data set peak lists. PUBLICATION
PINE-Sparky A SPARKY extension for the manual verification of PINE automated assignments. Now included in the NMRFAM-SPARKY Distribution. PUBLICATION
PINE-Sparky.2 PINE-SPARKY.2 is a project to provide graphical user interfaces to automate and visualize protein secondary structure assignments, hydrophobic core detection, 3-D structure calculation, resonance assignments and referencing error detection by a few clicks in NMRFAM-SPARKY which is one of the two main software packages (the other isPONDEROSA-C/S) in the Integrative NMR platform. Included in the NMRFAM-SPARKY.
Pulse Programs – Agilent The main emphasis of this pulse program library is directed towards protein and nucleic acids NMR spectroscopy of isotope enriched proteins in solution.

All pulse programs are written and tested on Varian VNS consoles running VnmrJ 2.1B and have been optimized for running on ColdProbes.

Pulse Programs – Bruker This pulse program library provides protein and nucleic acid solution NMR experiments for use in standard methods of spectral characterization, ligand binding and structure determination. Additional emphasis is given for isotopically enriched samples.

All pulse programs are written and tested for Bruker NMR spectrometers running Topspin 1.3 – 3.2 or XWin-NMR 3.5, with optimized parameters for CryoProbes.

PONDEROSA Peak picking Of NOE Data Enabled by Restriction Of Shift Assignments: a program for protein structure determination that utilizes information from prior assignments to automatically pick NOE peaks from 3D-NOESY (13C-edited and 15N-edited) spectra, with results used as input for a series of CYANA structure calculations. PUBLICATION
RNA-PAIRS RNA Probabilistic Assignment of Imino Resonance Shifts: a probabilistic algorithm for the automated assignment of RNA imino 1H and 15N resonances shifts, with conjoined determination and validation of secondary structure from input RNA sequence, and 1H-1H 2D-NOESY and 1H-15N 2D-HSQC spectra peak lists. PUBLICATION
rNMR An open source software package for visualizing and interpreting one and two dimensional NMR data specifically designed for high-throughput assignment and quantification of small molecules. Supports extensive batch manipulation of plotting parameters and has numerous tools for expediting repetitive resonance assignment and quantification tasks. PUBLICATION
NMRFAM Script Library A collection of scripts for NMR spectroscopists and general macromolecular structure research.
NMRFAM Virtual Machine

The Integrative NMR VM

Ubuntu Mate based Virtual Machine (VM) with pre-installed the latest versions of NMRFAM-Sparky, PyMOL, PONDEROSA-C/S packages.

A VM is an emulation of a computer operating system that can be installed and run on any different operating system. NMRFAM’s VM runs the Linux operating system Ubuntu. To run this on your Windows, Mac, or Linux computer, you will need to install VirtualBox (a virtualization software package from Oracle, freely available at www.virtualbox.org). You MUST have administrative privileges to install VirtualBox on your computer. For PCs, VirtualBox requires the enabling of virtualization in the BIOS.

NMRmix
A tool for the optimization of compound mixtures in 1D 1H NMR ligand affinity screens. PUBLICATION