DATA COLLECTION

As a premier NMR facility, NMRFAM seeks to maximize the efficiency and convenience of NMR data collection while minimizing cost and complications for the user.  As such, research and technology development for automated data collection methods are ongoing at NMRFAM, with two software packages described below.

 

ADAPT-NMR

ADAPT-NMR (Assignment-directed Data collection Algorithm utilizing a Probabilistic Toolkit in NMR) is a fully automated method for integration of protein NMR data collection, chemical shift assignment, and secondary structure determination.

ADAPT-NMR optimizes a fast data collection path involving multiple reduced dimensionality experiments so as to most efficiently realize complete resonance assignment and secondary structure determination of a protein while spectra are being collected on-the-fly.

With the sample in the NMR probe, ADAPT-NMR directs the NMR spectrometer to collect the optimal 2D plane of the most favorable experiment and then analyzes the resulting spectra to determine the positions of the peaks and to update the spins systems, chemical shift assignment, and the secondary structure of the protein. The procedure continues until the collected data support comprehensive peak identification, chemical shift assignments at the desired level of completeness, and protein secondary structure determination.

References


NMRbot

To facilitate the high-throughput acquisition of NMR experimental data on large sets of samples (such as for metabolites, ligand screenings or natural products research), we have developed NMRbot, a simple and straightforward automated methodology that capitalizes on recent advances in Bruker BioSpin NMR spectrometer hardware and software. Given the daunting challenge for non-NMR experts to collect quality spectra, our goal was to increase user accessibility, provide customized functionality, and improve the consistency and reliability of resultant data. NMRbot, is encoded in a set of scripts written in the Python programming language accessible within the Bruker BioSpin TopSpinTM software. NMRbot improves automated data acquisition and offers novel tools for use in optimizing experimental parameters on the fly. This automated procedure has been successfully implemented for investigations in metabolomics, small-molecule library profiling, and protein-ligand titrations on four Bruker BioSpin NMR spectrometers at the NMRFAM. The investigators reported benefits from ease of setup, improved spectral quality, convenient customizations, and overall time savings.

 Reference

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"The Future of NMR-Based Metabolomics, Current Opinion in Biotechnology (2017), pp. 34-40

Telluride School on Biomolecular Structure and Dynamics;Theory and Experiment (July 24-31, 2017) 

AMPERE NMR School (June 25th - July 1, 2017: Zakopane, Poland)

Documents on the use of the Bruker-Axs Nanostar,SAXS instrument and analysis of SAXS data are now available.

NMRFAM-SPARKY Distribution - the popular NMR analysis program SPARKY recompiled (including updated python and Tcl/Tk) with incorporation of PINE-Sparky, enhancements to import/export to the structural analysis program CYANA, and other useful python extensions.

ADAPT-NMR Enhancer: Complete Package for Reduced Dimensionality in Protein NMR Spectroscopy

RNA-PAIRS: RNA Probabilistic Assignment of Imino Resonance Shifts

PACSY, a Relational Database Management System for Protein Structure and Chemical Shift Analysis 

 

Donate to NMRFAM. US tax-deductible donation can be made to NMRFAM
Please write check payable to "UW Foundation, Account 112152802"  
And mail to: 
Attn: Sarah Lynn Traver Saunders
Associate Administrative Program Specialist 
University of Wisconsin-Madison 
433 Babcock Drive 
Madison, WI 53706 
Tel: 608-265-2507 or email 

 

1st: Lai Bergeman 
Rm 171; Phone 262-3173

2nd: Milo Westler
Rm B160; Phone 263-9599

3rd: Mark Anderson
Rm B224; Phone 265-3303

4th: Marco Tonelli
Rm B160; Phone 263-9493

5th: John Markley
Rm 171A; Phone 263-9349

We welcome your questions and feedback!

NMRFAM Established 1987