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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 Doreleijers at the Bijvoet Center for Biomolecular Research, Utrecht, The Netherlands. Current maintenance and expansion by Jurgen Doreleijers, BioMagResBank, University of Wisconsin-Madison, USA.
Keywords:
Analysis
NMR
(Ambiguous Restraints for Iterative Assignment) a software that automates NOE assignment and NMR structure calculation.
Keywords:
NMR
(Computer Aided Resonance Assignment) an application for the analysis of NMR spectra and computer-aided resonance assignment.
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NMR
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).
Keywords:
NMR
a graphical tool to construct chemical compound definitions for NMR, created to handle concepts like protonation variants and magnetic equivalence that are required for NMR resonance assignment. Several different chemical file formats are supported, including PDB, .mol and .mol2, but ChemBuild is special in its ability read and write CCPN chemical component XML files, which store NMR-aware information.
Keywords:
NMR
a program for non-linear least squares fitting of CPMG relaxation dispersion curves.
Keywords:
NMR
(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. Also includes CS-Rosetta toolbox, which provides useful scripts for preparing, running, and analyzing CS-Rosetta runs.
Keywords:
NMR
a program for the automated structure calculation of biological macromolecules on the basis of conformational constraints from NMR.

Restriction: available to users with an active CYANA software license.

Keywords:
NMR
a Perl program to assist in the analysis of laboratory frame spin relaxation data. It interfaces with ModelFree 4.01 (A. G. Palmer, Columbia University) and fully automates the process of model selection and tensor optimization.
Keywords:
NMR
(Function and Data Analysis) a program whose nmrPipeFit component is designed to analyse nD (n>1) NMR correlation spectra. The program is currently designed for arrayed 2D spectra, such as relaxation experiments and diffusion experiments, and simple 2D and 3D spectra.
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NMR
(General Approach to Magnetic resonance Mathematical Analysis) a package of C++ libraries that allow simulation of magnetic resonance (NMR, MRS) experiments. It is used for designing and analyzing NMR pulse sequences.
Keywords:
NMR
(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.
a computer program intended for the calculation of NMR relaxation of small, quasirigid macromolecules whose structure, with atomic resolution, is taken from a PDB file of atomic coordinates. The basic hydrodynamic quantities involved in dynamic NMR are evaluated in the same fashion as in the closely related HYDROPRO program. HYDRONMR then calculates NMR quantities, like T1, T2, NOE,. for each residue of a globular ...
Keywords:
NMR
an algorithm to reconstruct non-uniformly acquired NMR data.
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NMR
(Multiscale Modeling Tools for Structural Biology) a collection of perl-based user-level utilities as well as programming libraries for multiscale protein structure modeling. Intended applications include protein structure prediction, loop modeling, structure refinement, and structure evaluation/scoring.
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.
Keywords:
NMR
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.
Keywords:
NMR
an open source software to analyse NMR relaxation dispersion data of either CPMG or R1p (R1rho) dispersion experiments. The graphical interface enables simple management of large experimental data sets and simple and automated analysis. NESSY autamatically calculates effective transverse relaxation rate (R2eff) and performs model selection between different relaxation dispersion models.
Keywords:
NMR
is a new version of Sparky renamed because NMRFAM has taken over the original Sparky to support advances in the biomolecular NMR field. Tom Ferrin and Tom Goddard of UCSF, generously allowed NMRFAM to develop this the original Sparky, which remains the most popular NMR biomolecular analysis tool available.
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NMR
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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NMR
used to visualize and Analyze Nuclear Magnetic Resonance Data.
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NMR
(Prediction of ALignmEnt from Structure) a software for the analysis of residual dipolar couplings and for the prediction of the magnitude and orientation of a sterically induced alignment tensor from a solute's (protein/nucleic acid/oligosaccharide) three-dimensional shape.
Keywords:
Bioinformatics
NMR
a C/C++ computer program originally developed as a universal coordinate and protein NMR restraint converter. Its primary function is to provide a user-friendly tool for interconverting between protein coordinate and protein NMR restraint data formats. It also provides an integrated set of computational methods for protein NMR restraint analysis and structure quality assessment, relabeling of prochiral atoms with correct IUPAC names, as well ...
performs conversions of spectra from NMRPipe to XEASY format. Pipe2xeasy can read the ASCII file with header information, which is produced with "showhdr -verb filename".
Keywords:
NMR
a software toolkit and library of routines for the analysis and manipulation of macromolecular structural models, implemented in the Python programming language.
(Protein NMR backbone resonance assignment) uses structure-based chemical shift predictions to solve the backbone resonance assignment problem in protein NMR spectroscopy. This enables rapid determination of highly accurate assignments on the basis of minimal experimental datasets, even for spectroscopically challenging proteins. RASP takes as input spin systems assembled on the basis of an arbitrary set of conventional triple-resonance NMR experiments. Uniquely, RASP is capable ...
Keywords:
NMR
a residual dipolar coupling analysis tool. For-profit users interested in using this tool should contact Homayoun Valafar at hvalafar@gmail.com to inquire.
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NMR
a program for adding hydrogens to a Protein DataBank (PDB) molecular structure file. Hydrogens are added in standardized geometry with optimization of the orientations of OH, SH, NH3+, Met methyls, Asn and Gln sidechain amides, and His rings. Both proteins and nucleic acids can be processed. HET groups can also be processed as long as the atom connectivity is provided.
Keywords:
Crystallography
NMR
a software package designed for the study of molecular dynamics by NMR data analysis.
Keywords:
NMR
converts PDB files between PDBv2.3 and PDBv3.2 formats. It can accurately and rapidly convert in either direction: old to new OR new to old. Atom records of type ATOM, HETATM, TER, ANISOU, SIGATM, SIGUIJ, and LINK are converted, as are DNA residue names (e.g., A, C, T, G of v2.3 cf. DA, DC, DT, DG of v3.2).
predicts the backbone and side chain 1H, 13C and 15N chemical shifts for proteins using their structural (PDB) coordinates as input.
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NMR
(Sparse Multidimensional Iterative Lineshape Enhanced) a NMRPipe processing function whose algorithm integrates a priori information about NMR signals for most robust reconstruction of non-uniformly sampled (NUS) multidimensional data.
Keywords:
NMR
a graphical NMR assignment and integration program for proteins, nucleic acids, and other polymers.
Keywords:
NMR
provides a fast way to visualise NMR spectrum and peak data. It supports 2D and 3D graphical display modes for multidimensional and simple 1D spectra. SpecView can automatically import spectra and peaks from many different file formats without user intervention. Spectra may be frequency referenced and superposed within the program.
Keywords:
NMR
predicts protein backbone and sidechain torsion angles from NMR chemical shifts
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NMR
a program that allows the determination of rotational diffusion from three-dimensional structure coordinates and experimental 15N relaxation data, and now allows 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 or anisotropic rotational diffusion tensor.
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NMR
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.
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NMR
a program for interactive, computer-supported NMR spectrum analysis.
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NMR
a generalized package for biomolecular structure determination from experimental NMR data combined with known geometric data. Xplor–NIH was originally derived from XPLOR version 3.851 and contains all of the functionality therein while also incorporating numerous completely new features designed to render its overall architecture highly flexible and to foster the rapid and easy development of new and improved functionality. This architecture is ...
Keywords:
NMR
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