Useful software
Xplor-NIH: The Xplor-NIH NMR structure determination package is a program developed in NIDDK which is distributed freely to academia from the NIH/NIDDK web site
Schwieters, C.D., Kuszewski, J., Tjandra, N. & Clore, G.M. (2003) The Xplor-NIH NMR molecular structure determination package. J. Magn. Reson. 160, 66-74. Pubmed PDF
Schwieters, C.D., Kuszewski, J. & Clore, G.M. (2006) Using Xplor-NIH for NMR molecular structure determination. Progr. NMR Spectroscopy 48, 47-62. PDFSome example input files (please acknowledge source of scripts)
VMD-XPLOR: The VMD-XPLOR NMR Graphics package interfaced with Xplor-NIH and developed in NIDDK which is distributed freely to academia from the NIH/NIDDK web site
Schwieters, C.D. & Clore, G.M. (2001) The VMD-XPLOR visualization package for NMR structure refinement. J. Magn. Reson.149, 239-244. pubmed PDFSome example input files to create reweighted atomic probability density maps from an ensemble of structures.
Schwieters, C.D. & Clore, G.M. (2002) Reweighted atomic densities to represent ensembles of NMR structures. J. Biomol. NMR 23, 221-225. Pubmed PDF
OtherNMR related software: STEREOSEARCH Grid search program for obtaining stereoassignments.
Nilges, M., Clore, G.M. & Gronenborn, A.M. (1990) 1H-NMR stereospecific assignments by conformational database searches. Biopolymers 29, 813-822. pubmed PDF
1H and 13C shift probabilities in proteins
TORSION ANGLE CORRELATIONS
protein phi/psi 2D torsion angle database potential surfaces
protein sidechain 2D torsion angle database potential surfaces
nucleic acid (DNA and RNA combined) 2D torsion angle database potential surfaces
Spin_Label_Build: scripts for building on spin labels in Xplor-NIH.
Fawzi, N.L., Fleissner, M.R., Anthis, N.J., Kalai, T., Hideg, K., Hubbell, W.L. & Clore, G.M. (2011) A rigid disulfide-linked nitroxide side chain simplifies the quantitative analysis of PRE data. J. Biomol. NMR 51, 105-114. Pubmed PDF
The tar file contains all relevant scripts and a README file.
METHYL_PRE_ASSIGN: Automated PRE-based assignment of methyl groups based on a known structure.
Venditti, V., Fawzi, N.L. & Clore, G.M. (2011) Automated sequence- and stereo-specific assignment of methyl-labeled proteins by paramagnetic relaxation and methyl-methyl nuclear Overhauser enhancement spectroscopy. J. Biomol. NMR 51, 319-328. Pubmed PDF Supplementary
The tar file contains all relevant scripts and programs for automated assignment of methyl groups based on PRE data and a known structure. Once the three step PRE assignment procedure has been carried out, the resulting assignments can be confirmed by analysis of a 4D methyl-methyl NOE spectrum. NOE raw data
ILVA methyl-labeled 4D 13C-HMQC-NOE-HMQC pulse sequence and 4D HC(CO)NH-TOCSY pulse sequenceDEST FITTING PROGRAMS
Fawzi, N.L., Ying, J., Ghirlando, R, Torchia, D.A. & Clore, G.M. (2011) Atomic resolution dynamics on the surface of amyloid ß protofibrils probed by solution NMR. Nature 480, 268-272. pubmed PDF Supplementary Software for fitting DEST dataFawzi, N.L., Ying, J., Torchia, D.A. & Clore, G.M. (2012) Probing exchange kinetics and atomic resolution dynamics in high molecular weight complexes: dark-state exchange saturation transfer NMR spectroscopy. Nature Protocol 7, 1523-1533. pubmed PDF
DESTfitting_v1.9
The tar files contains all relevant scripts, programs, and helper files for fitting DEST and DeltaR2 data.
Pulse sequence and processing scripts for 15N-DEST and 15N-R2 experiments on Bruker AV900 spectrometer:ILV_HMCMCBCACO_SIM pulse sequence
Tugarinov, V., Venditti, V. & Clore, G.M. (2013) A NMR experiment for simultaneous correlations of valine and leucine/isoleucine methyls with carbonyl chemical shifts in proteins. J. Biomol. NMR 58, 1-8. Pubmed PDF SupplementaryIncludes Bruker pulse sequence and all associated files in add_files directory (e.g. for shaped pulses, etc....).
Calculating protein concentration from absorbance at 205 nm
Anthis, N.J. & Clore, G.M. (2013) Sequence-specific determination of protein and peptide concentrations by absorption at 205 nm, Protein Science, 22, 851-858. Pubmed PDF
Calculating PRE rates
Anthis, N.J. & Clore, G.M. (2015) Visualizing transient dark states by NMR spectroscopy. Q. Rev. Biophys. 48, 35-116. Pubmed PDF
Software from the Bax group in NIDDK/NIH
includes NMRPipe, TALOS, SSIA, PALES and ACME
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