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 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.

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ARIA

- (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 Fran├žois-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.

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CARA

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

yes yes yes

CcpNmr

- 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).

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CPMGFit

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

yes yes yes

CS-ROSETTA

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. This software is computationally intensive and would ideally be run on a cluster. The University of Wisconsin hosts a [web front end for CS-Rosetta][1] that runs jobs on the Open Science Grid (100k+ CPUs) and is free for academic users. [1]: https://condor.bmrb.wisc.edu/rosetta/

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CYANA

- a program for the automated structure calculation of biological macromolecules on the basis of conformational constraints from NMR. <br><br> CYANA is a commercial software application that we can include in your installation for ease of use, but that requires you or your institute to have a current license in place. To enable the SBGrid installation for CYANA please send an email to <a href = "mailto:licensing@sbrid.org">licensing@sbgrid.org</a> with information confirming that your license is active. <br><br>

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HADDOCK

- (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.

yes yes yes

ModelFree

- 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.

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MODULE

- 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.

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NMRPipe

- 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.

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NMRVIEW

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

yes yes yes

Prediction of ALignmEnt from Structure (PALES)

- 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.

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REDCAT

a residual dipolar coupling analysis tool. For-profit users interested in using this tool should contact Homayoun Valafar at hvalafar@gmail.com to inquire.

yes yes yes

relax

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.

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Sparky

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

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TENSOR

- 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.

yes yes yes

Wattos

- 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.

yes yes

XEASY

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

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Xplor-NIH

- a system for X-ray crystallography and NMR.

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