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Name Description Links
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,
(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
a series of programs for macromolecular NMR including AnalysisAssign, AnalysisScreen, AnalysisMetabolomics and AnalysisStructure, and with version 3, the addition CcpNmr ChemBuild.
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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.
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NMR
an analysis program for chemical exchange detected by NMR.
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NMR
a program for non-linear least squares fitting of CPMG relaxation dispersion curves.
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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.
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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.
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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.
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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 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. HYDRONMR evaluates basic hydrodynamic quantities involved in dynamic NMR in the same fashion as HYDROPRO program, then calculates NMR quantities (T1, T2, NOE, etc) for each residue of a globular protein and reports the translational diffusion coefficient, …
Keywords:
NMR
(Intrinsically Disordered Proteins Conformer Generator) a flexible, modular platform for generating ensembles of disordered protein states that builds conformers by sampling backbone torsion angles of relevant sequence fragments extracted from protein structures in the RCSB Protein Data Bank.
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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.
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NMR
a new version of Sparky renamed because NMRFAM, through the generous allowance of Tom Ferrin and Tom Goddard of UCSF, has taken over the original Sparky for continuous development to support advances in the biomolecular NMR field.
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NMR
a software for processing multi-dimensional NMR spectra featuring quality and performance to handle complex data analyses.
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NMR
a python module for reading, writing, and interacting with the spectral data stored in a number of common NMR data formats.
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
an easy-to-use software package for the two-dimensional lineshape analysis of titration experiments.
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NMR
a tool used to visualize and Analyze Nuclear Magnetic Resonance Data.
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NMR
a tool used to visualize and Analyze Nuclear Magnetic Resonance Data.
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NMR
a new user-friendly method built for automatic Δχ-tensor determination.
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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:
NMR
a python module for calculating paramagnetic effects in NMR spectra of proteins. This currently includes fitting of paramagnetic susceptibility tensors to experimental data associated with pseudocontact shifts (PCS) residual dipolar couplings (RDC), paramagnetic relaxation enhancements (PRE) and cross-correlated relaxation (CCR). A GUI allows easy viewing of data and seamless transition between PCS/RDC/PRE/CCR calculations.
Keywords:
NMR
a C/C++ application developed as a coordinate and protein NMR restraint converter. This user-friendly tool provides an integrated set of computational methods for protein NMR restraint analysis and structure quality assessment, relabeling of prochiral atoms with correct IUPAC names, and analysis of atomic position consistency based on their convergence across a protein NMR ensemble.
a tool that performs conversions of spectra from NMRPipe to XEASY format. It can read the ASCII file with header information, which is produced with "showhdr -verb filename".
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NMR
a software suite for multidimensional NMR and 3D structure calculation of biomolecules.
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NMR
a newly designed NMR chemical shift guided protein structure alignment method to generate protein templates with the best matched local structure from the Protein Data Bank.
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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) a tool that uses structure-based chemical shift predictions to solve the backbone resonance assignment problem in protein NMR spectroscopy to enable rapid determination of highly accurate assignments on the basis of minimal experimental datasets, even for spectroscopically challenging proteins.
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.
a software package designed for the study of molecular dynamics by NMR data analysis.
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NMR
a tool that 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).
a program that 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
a graphical NMR assignment and integration program for proteins, nucleic acids, and other polymers.
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NMR
a tool that provides a fast way to visualize NMR spectrum and peak data. It supports 2D and 3D graphical display modes for multidimensional and simple 1D spectra. Can automatically import spectra and peaks from many different file formats without user intervention. Spectra may be frequency referenced and superposed within the program.
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NMR
a tool that 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 program that performs automated NMR data analysis for protein 3D structure determination. It represents the result of more than a decade of innovative research performed in order to enable accurate, objective and highly automated protein structure determination by 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 package for biomolecular structure determination from experimental NMR data combined with known geometric data. Xplor–NIH was derived from XPLOR version 3.851 and contains all of the functionality therein in addition to numerous new features designed to render a highly flexible architecture and foster the rapid and easy development of new functionality.
Keywords:
NMR
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