NMR Methods

SBGrid supports 20 nmr methods software titles. The following software packages are supported by SBGrid; availability of a specific software package may be limited based on license requirements.

Software Title Description Linux 32-bit Linux 64-bit OS X Intel Links

AQUA

- a suite of programs that analyze the quality of biomolecular structures determined via NMR spectroscopy. AQUA was ...

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  • a suite of programs that analyze the quality of biomolecular structures determined via NMR spectroscopy. AQUA was initially developed by Ton Rullmann and Jurgen Doreleijersb Bijvoet Center for Biomolecular Research, Utrecht, The Netherlands. Current maintenance and expansion by Jurgen Doreleijers, BioMagResBank, University of Wisconsin-Madison, USA.

Developers

Jurgen Doreleijers

Categories

NMR Methods

Structure Analysis

Versions

Citations

Laskowski R.A., Rullmann J.A.C., MacArthur M.W., Kaptein R. & Thornton J.M. (1996). "AQUA and PROCHECK-NMR: Programs for checking the quality of protein structures solved by NMR". J. Biomol. NMR 8, 477-486.

Doreleijers J.F., Rullmann J.A.C. & Kaptein R. (1998). "Quality assessment of NMR structures: a statistical survey". J. Mol. Biol. (1998) 281:149-164.

Doreleijers J.F., Raves M.L., Rullmann J.A.C. & Kaptein R. (1999). "Completeness of NOEs in proteins, a statistical analysis of NMR data". J. Biomol. NMR (1999) 14, 123-132.


Static link to the SBGrid AQUA page.

ARIA

- (Ambiguous Restraints for Iterative Assignment) is a software that automates NOE assignment and NMR structure calculation. ARIA ...

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  • (Ambiguous Restraints for Iterative Assignment) is a software that automates NOE assignment and NMR structure calculation.

ARIA was originally developed in Michael Nilges's team at the European Molecular Biology Laboratory, Heidelber by François-Regis Chalaoux, Dinu Gherman, Jens Linge, Michael Nilges and Sean O'Donoghue. Since 2001, BIS (Bioinformatique Structurale) team, and specifically Michael Habeck and Wolfgang Rieping, Institut Pasteur, in Paris.

Developers

Benjamin Bardiaux

Therese Malliavin

Categories

NMR Methods

Versions

Citations

Rieping et al. ARIA2: automated NOE assignment and data integration in NMR structure calculation. Bioinformatics (2007) vol. 23 (3) pp. 381-2


Static link to the SBGrid ARIA page.

CARA

- an application for the analysis of NMR spectra and compute- aided resonance assignment.

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  • an application for the analysis of NMR spectra and compute- aided resonance assignment.

Developers

Pascal Bettendorff

Rochus Keller

Fred Damberger

Categories

NMR Methods

Versions

Citations

Please reference the book The Computer Aided Resonance Assignment Tutorial by Rochus Keller. Alternatively you can cite Rochus' PhD thesis, Diss. ETH Nr. 15947. It would also be helpful if you could mention in your publication that CARA can be downloaded from cara.nmr.ch


Static link to the SBGrid CARA page.

CcpNmr

- an analysis program built on top of the CCP Data Model, inspired partly by the program ANSIG ...

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  • an analysis program built on top of the CCP Data Model, inspired partly by the program ANSIG (Per Kraulis) and partly by the program Sparky (T.D.Goddard and D.G.Kneller, UCSF).

Developers

Wayne Boucher

Rasmus Fogh

Categories

NMR Methods

Versions

Citations

Vranken et al. The CCPN data model for NMR spectroscopy: development of a software pipeline. Proteins (2005) vol. 59 (4) pp. 687-96


Static link to the SBGrid CcpNmr page.

CPMGFit

- a program for non-linear least squares fitting of CPMG relaxation dispersion curves.

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  • a program for non-linear least squares fitting of CPMG relaxation dispersion curves.

Developers

Arthur Palmer

Categories

NMR Methods

Versions


Static link to the SBGrid CPMGFit page.

CS-ROSETTA

- (Chemical-Shift-ROSETTA) a robust protocol to exploit mining of protein chemical shifts deposited in the BMRB, in conjunction ...

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  • (Chemical-Shift-ROSETTA) a robust protocol to exploit mining of protein chemical shifts deposited in the BMRB, in conjunction with the known corresponding 3D structures for de novo protein structure generation, using as input parameters the 13CA, 13CB, 13C', 15N, 1HA and 1HN NMR chemical shifts.

Developers

Ad Bax

Categories

NMR Methods

Versions

Citations

Shen et al. De novo protein structure generation from incomplete chemical shift assignments. J Biomol NMR (2009) vol. 43 (2) pp. 63-78


Static link to the SBGrid CS-ROSETTA page.

CYANA

- a program for the automated structure calculation of biological macromolecules on the basis of conformational constraints from ...

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  • a program for the automated structure calculation of biological macromolecules on the basis of conformational constraints from NMR.

Developers

L.A.Systems, Inc.

Peter Güntert

Categories

NMR Methods

Versions

Citations

Güntert. Automated NMR structure calculation with CYANA. Methods Mol Biol (2004) vol. 278 pp. 353-78

Technical Notes

CYANA is commercial software and is licensed on a per-lab basis. Once you have purchased a license, please contact us to let us know, and we will be able to remotely install the software for your lab.


Static link to the SBGrid CYANA page.

DYANA

- a program for NMR structure calculation based on a highly efficient implementation of torsion angle dynamics. It ...

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  • a program for NMR structure calculation based on a highly efficient implementation of torsion angle dynamics. It is the successor of DIANA, the first program package for NMR structure calculation developed by P. Güntert. DYANA is no longer available or supported. Its functionality has been incorporated into the program package CYANA.

Developers

Peter Guentert

Categories

NMR Methods

Versions

Citations

Güntert et al. Torsion angle dynamics for NMR structure calculation with the new program DYANA. J Mol Biol (1997) vol. 273 (1) pp. 283-98


Static link to the SBGrid DYANA page.

HADDOCK

- (High Ambiguity Driven biomolecular DOCKing) relies on an approach that makes use of biochemical and/or biophysical interaction ...

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  • (High Ambiguity Driven biomolecular DOCKing) relies on an approach that makes use of biochemical and/or biophysical interaction data, such as chemical shift perturbation data resulting from NMR titration experiments, mutagenesis data or bioinformatic predictions. HADDOCK was written by Alexandre Bondvin is derived from ARIA scripts by Michael Nilges and Jens Linge.

Developers

Alexandre Bonvin

Categories

NMR Methods

Computational Chemistry

Versions

Citations

de Vries et al. HADDOCK versus HADDOCK: new features and performance of HADDOCK2.0 on the CAPRI targets. Proteins (2007) vol. 69 (4) pp. 726-33

Dominguez et al. HADDOCK: a protein-protein docking approach based on biochemical or biophysical information. Journal of the American Chemical Society (2003) vol. 125 (7) pp. 1731-7


Static link to the SBGrid HADDOCK page.

ModelFree

- a program to fit the extended model free spectral density function to NMR spin relaxation data. The ...

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  • a program to fit the extended model free spectral density function to NMR spin relaxation data. The program can analyze the spin-lattice relaxation rate constant (R1), the spin-spin relaxation rate constant (R2), and the heteronuclear steady-state {1H}-X nuclear Overhauser effect (NOE) for any combination of 13C and 15N spins at up to five static magnetic fields.

Developers

Arthur Palmer

Categories

NMR Methods

Versions

Citations

Mandel et al. Backbone dynamics of Escherichia coli ribonuclease HI: correlations with structure and function in an active enzyme. Journal of molecular biology (1995) vol. 246 (1) pp. 144-63


Static link to the SBGrid ModelFree page.

MODULE

- a novel program developed to allow the determination of alignment tensor parameters for individual or multiple domains ...

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  • a novel program developed to allow the determination of alignment tensor parameters for individual or multiple domains in macromolecules from residual dipolar couplings and to facilitate their manipulation and construct low-resolution models of macromolecular structure.

Developers

Martin Blackledge

Categories

NMR Methods

Versions

Citations

1.0: Dosset et al. Novel Interactive Tool for Rigid-Body Modeling of Multi-Domain Macromolecules using Residual Dipolar Couplings. J.Biomol. NMR. 2001. 20:223-231.

2.0: Dosset et al. Efficient analysis of macromolecular rotational diffusion from heteronuclear relaxation data. Biomol.NMR. 2000. 16: 23-28.


Static link to the SBGrid MODULE page.

NMRPipe

- a set of comprehensive facilities for Fourier processing of spectra in one to four dimensions, as well ...

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  • a set of comprehensive facilities for Fourier processing of spectra in one to four dimensions, as well as a variety of facilities for spectral display and analysis. This is the official NMRScience version of NMRPipe.

Developers

Frank Delaglio

Ad Bax

Categories

NMR Methods

Versions

Citations

Delaglio et al. NMRPipe: a multidimensional spectral processing system based on UNIX pipes. Journal of biomolecular NMR (1995) vol. 6 (3) pp. 277-93

Frank Delagio is no longer managing distribution or support. For distribution, licensing, permissions, email Ad Bax bax@nih.gov, for support contact Teddy Zartler at teddy@quantumtessera.com . To download the software: http://spin.niddk.nih.gov/NMRPipe/install/

Technical Notes

SBGrid has a site license that covers all participating laboratories.


Static link to the SBGrid NMRPipe page.

NMRVIEW

- is used to visualize and Analyze Nuclear Magnetic Resonance Data.

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  • is used to visualize and Analyze Nuclear Magnetic Resonance Data.

Developers

Bruce Johnson

Categories

NMR Methods

Versions

Citations

Bruce A. Johnson, Richard A. Blevins, NMR View: A computer program for the visualization and analysis of NMR data, Journal of Biomolecular NMR, Volume 4, Issue 5, Sep 1994, Pages 603 - 614. DOI 10.1007/BF00404272, URL http://dx.doi.org/10.1007/BF00404272


Static link to the SBGrid NMRVIEW page.

Prediction of ALignmEnt from Structure (PALES)

- a software for the analysis of residual dipolar couplings. Its main component is the PALES (Prediction of ...

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  • a software for the analysis of residual dipolar couplings. Its main component is the PALES (Prediction of ALignmEnt from Structure) simulation that predicts the magnitude and orientation of a sterically induced alignment tensor from a solute's (protein/nucleic acid/oligosaccharide) three-dimensional shape.

Developers

Markus Zweckstetter

Categories

NMR Methods

Versions

Citations

Zweckstetter. NMR: prediction of molecular alignment from structure using the PALES software. Nature protocols (2008) vol. 3 (4) pp. 679-90

Zweckstetter et al. Prediction of charge-induced molecular alignment of biomolecules dissolved in dilute liquid-crystalline phases. Biophysical journal (2004) vol. 86 (6) pp. 3444-60


Static link to the SBGrid Prediction of ALignmEnt from Structure (PALES) page.

relax

Molecular dynamics by NMR data analysis. relax is a program designed for the study of the dynamics of ...

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Molecular dynamics by NMR data analysis. relax is a program designed for the study of the dynamics of proteins or other macromolecules though the analysis of NMR relaxation experiments. It supports exponential curve fitting for the calculation of the R1 and R2 relaxation rates, calculation of the NOE, reduced spectral density mapping, the Lipari and Szabo model-free analysis, study of domain motions via the N-state model and frame order dynamics theories using anisotropic NMR parameters such as RDCs and PCSs, and the investigation of stereochemistry.

Developers

Edward d'Auvergne

Categories

NMR Methods

Versions

Citations

d'Auvergne and Gooley. Optimisation of NMR dynamic models I. Minimisation algorithms and their performance within the model-free and Brownian rotational diffusion spaces. Journal of biomolecular NMR (2008) vol. 40 (2) pp. 107-19

d'Auvergne and Gooley. Optimisation of NMR dynamic models II. A new methodology for the dual optimisation of the model-free parameters and the Brownian rotational diffusion tensor. Journal of biomolecular NMR (2008) vol. 40 (2) pp. 121-33


Static link to the SBGrid relax page.

Sparky

- a graphical NMR assignment and integration program for proteins, nucleic acids, and other polymers.

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  • a graphical NMR assignment and integration program for proteins, nucleic acids, and other polymers.

Developers

Sparky Developer Group

Thomas Goddard

Categories

NMR Methods

Versions

Citations

Unpublished, but please cite as follows: T. D. Goddard and D. G. Kneller, SPARKY 3, University of California, San Francisco.


Static link to the SBGrid Sparky page.

TENSOR

- allows the determination of rotational diffusion from three-dimensional structure coordinates and experimental 15N relaxation data, and nowallows ...

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  • allows the determination of rotational diffusion from three-dimensional structure coordinates and experimental 15N relaxation data, and nowallows a rigorous model-free analysis of local internal mobility affecting backbone amides, from 15N {R1,R2,nOe} relaxation rates in the presence of an isotropic of anisotropic rotational diffusion tensor.

Developers

Martin Blackledge

MODULE Team

Categories

NMR Methods

Versions

Citations

Efficient analysis of Macromolecular Rotational Diffusion from Heteronuclear Relaxation Data Dosset, P.; Hus, J-C; Blackledge, M.; Marion, D. J.Biomol.NMR. 16:23-28, January 2000.


Static link to the SBGrid TENSOR page.

Wattos

- a collection of Java programs for structural biology and NMR spectroscopy that analyze, annotate, parse, archive, and ...

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  • a collection of Java programs for structural biology and NMR spectroscopy that analyze, annotate, parse, archive, and disseminate experimental NMR data deposited by authors worldwide into the PDB and BMRB.

Developers

Jurgen Doreleijers

Categories

NMR Methods

Versions

Citations

Doreleijers et al. BioMagResBank databases DOCR and FRED with converted and filtered sets of experimental NMR restraints and coordinates from over 500 protein PDB structures. J. Biomol. NMR. 2005. 32: 1-12.

Nederveen et al. RECOORD: a recalculated coordinate database of 500+ proteins from the PDB using restraints from the BioMagResBank. Proteins. 2005. 59: 662-672.

Nabuurs et al. DRESS: a database of REfined solution NMR structures. Proteins. 2004. 55: 483-486.

Doreleijers et al. The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. J. Biomol. NMR. 2003. 26: 139-146.


Static link to the SBGrid Wattos page.

XEASY

- a program for interactive, computer-supported NMR spectrum analysis.

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  • a program for interactive, computer-supported NMR spectrum analysis.

Developers

Sharron Thomas

Kurt Wuthrich

Categories

NMR Methods

Versions

Citations

Bartels C et al. The program XEASY for computer-supported NMR spectral analysis of biological macromolecules. J. Biomol. NMR. 1995. 6: 1–10.

Technical Notes

Start the vncserver & vncviewer

vncserver :5 -cc 3 -depth 8 -localhost -geometry 1252x934
vncviewer :5

When the viewer window closes, the vncserver will be killed

vncserver -kill :5
to reset password remove .vnc directory from your HOME



Static link to the SBGrid XEASY page.

Xplor-NIH

- a system for X-ray crystallography and NMR.

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  • a system for X-ray crystallography and NMR.

Developers

Charles Schwieters

Categories

NMR Methods

Versions

Citations

Schwieters CD et al. The Xplor-NIH NMR Molecular Structure Determination Package. J. Magn. Res. 2003. 160: 66-74.

Schwieters CD. Using Xplor-NIH for NMR molecular structure determination. Progr. NMR Spectroscopy. 2006. 48: 47-62.


Static link to the SBGrid Xplor-NIH page.