NMRFAM Software & Pulse Program libraries

NMRFAM Software

Software Overview Chart

figure by L. Clos

Current Software

PINE – Automatic backbone and sidechain assignments, detection and automated correction of potential referencing problems or inconsistent assignments and secondary structure determination. Accepts, as input, the sequence of the protein plus peak lists from a variety of NMR experiments.

NMRFAM Sparky Distribution is a distribution of the popular NMR analysis program SPARKY with incorporation of PINE-Sparky, enhancements to import/export to the structural analysis program CYANA, and other python extensions. Versions are available for download on Window, Linux, and MacOS platforms.

PINE-Sparky is a Sparky extension for the manual verification of the automated assignments supplied by PINE. It has been incorporated into the NMRFAM Sparky distribution.

rNMR - the new small molecule visualization and quantification tool

FMQ_data – This link will redirect you to the rNMR home page, which contains the data and analysis used in: I.A. Lewis et al, Anal. Chem. 2007 December 15; 79(24): 9385-9390

PISTACHIO – making backbone and side chain assignments – now included in PINE

PECAN - secondary structure predictions – now included in PINE

LACS - Detection and automated correction of potential referencing problems and detection of inconsistent assignments  - now included in PINE

HIFI-NMR – adaptive approach for rapid and automated collection of NMR data

RNA-PAIRS – (RNA Probabilistic Assignment of Imino Resonance Shifts) Automatic assignment of RNA imino ¹H and ¹⁵N resonances shifts, with conjoined determination of secondary structure.  Accepts, as input, the RNA sequence and peak lists from ¹H-¹H 2D NOESY and ¹H-¹⁵N 2D HSQC experiments.

NMRFAM Pulse Program Libraries

NMRFAM Bruker Pulse Programs

NMRFAM Varian Pulse Programs

HSQC₀- In the download zip file, there are 6 pulse sequence files, 3 for non-constant time (HSQC1, HSQC2 and HSQC3) and 3 for constant time (HSQC1, HSQC2 and HSQC3) and an instruction file on how to set up the experiments. (Kaifeng Hu, William M. Westler, and John L. Markley, Simultaneous quantification and identification of individual chemicals in metabolite mixtures by two-dimensional extrapolated time-zero ¹H-¹³C HSQC (HSQC₀), (2011) J. Am. Chem. Soc., 133(6), 1662-5.)