Open Source Software for NMR Data AnalysisrNMR
Open Source Software for NMR Data Analysis - rnmr.nmrfam.wisc.edu
NMRbox is a resource for biomolecular NMR (Nuclear Magnetic Resonance) software.
4DSPOT
Protein chemical shift prediction in 4-dimensions, with molecular flexibility as the 4th dimension
ABACUS
Combines assignment of protein NOESY spectra and structure determination
ADAPT-NMR Enhancer
Visualize the tilted 2D plane data from ADAPT-NMR
AFNMR
Quantum chemical estimates chemical shifts in proteins and nucleic acids
ALATIS
A tool for assigning unique and reproducible labels to all atoms of small molecules
ALMOST
All atom molecular simulation toolkit
AlphaFold
Neural network prediction of protein structure
Amaterasu
Simplify the screening, acquisition, processing and model fitting of R1ρ relaxation dispersion NMR datasets
Amaterasu'kai
Simplify the screening, acquisition, processing and model fitting of R1ρ relaxation dispersion NMR datasets
AmberTools
Amber is a set of molecular mechanical force fields and a package of molecular simulation programs
ANATOLIA
NMR software for spectral analysis of total lineshape
ANSURR
ANSURR uses backbone chemical shifts to validate the accuracy of a protein structure
AQUA
AQUA is a suite of programs for Analyzing the QUAlity of biomolecular structures
ARIA
Automates NOE assignment and NMR structure calculation
ArShift
Structure based predictor of protein aromatic side-chain proton chemical shifts
ASDP
Automated determination of protein structures and NOE assignments from NMR data
Assign_SLP
Genetic algorithm search for correct assignments of HSQC crosspeaks
ATSAS
A program suite for small-angle scattering data analysis from biological macromolecules
AutoAssign
Automating the analysis of backbone resonance assignments
AutoDock Vina
An open-source program for doing molecular docking
Azara
A suite of programs to process and view NMR data
BATMAN
An R package for estimating metabolite concentrations from NMR spectral data using a specialised MCMC algorithm
BLAST
Finds regions of similarity between biological sequences
BLAST (legacy version)
Finds regions of similarity between biological sequences
CS-Rosetta (BMRB)
Submission tool for sending jobs to the BMRB CS-Rosetta server
calRW
Distance-dependent atomic potential for protein structure modeling and structure decoy recognition
calRW+
Orientation-dependent atomic potential for protein structure modeling and structure decoy recognition
CambridgeCS
Reconstruction of non-uniform spectra with compressed sensing
CAMERA
Maximum Entropy reconstruction of nonuniformly sparsely sampled data
CARA
The analysis of NMR spectra and computer aided resonance assignment
Carma
Analysis of molecular dynamics trajectories
CATIA
Analyze CPMG relaxation dispersion data and extract chemical exchange parameters of a two-site chemically exchanging system
CcpNmr Analysis
An NMR spectrum visualisation, resonance assignment and data analysis program
CcpNmr Analysis Assign
An NMR spectrum visualisation, resonance assignment and data analysis program
CcpNmr Analysis Metabolomics
Module of CcpNmr Analysis for analyzing metabolomics data
CcpNmr Analysis Screen
Module of CcpNmr Analysis for screening
CcpNmr ChemBuild
A graphical tool to construct chemical compound definitions for NMR
CcpNmr SpecView
SpecView provides a fast and easy way to visualize NMR spectrum and peak data
CH3Shift
Structure-based prediction of protein methyl group chemical shifts
CHEMEX
Fit chemical exchange induced shift and relaxation data
Chimera
An extensible interactive molecular visualization and analysis system
CLUSTAL W/X
Multiple alignment of nucleic acid and protein sequences
Cluster 3.0
Clustering software for gene expression and data analysis
CNS v1.3, 1.21-ARIA
Provides a hierarchical approach for the most commonly used algorithms in structure determination
COMPASS
Experimental protein structure verification by scoring with a single, unassigned NMR spectrum
CONNJUR Workflow Builder
An open-source framework for software and data integration in bio-NMR
Connjur Widgets
Widgets built into the File Browser for parsing NMR metadata
CPMG-Fit (Korzhnev)
Fits CPMG relaxation dispersion data for analysis of chemical exchange in NMR spectroscopy
CPMGFit (Palmer)
Fits CPMG relaxation dispersion data for analysis of chemical exchange in NMR spectroscopy
CSCDP
Chemical shift calculation for chemically denatured proteins
CS-GAMDy
A robust algorithm for refining protein structures with NMR chemical shifts
CS-Rosetta
System for chemical shifts based protein structure prediction using ROSETTA
CTFFIND
Program for finding CTFs of electron micrographs
CYRANGE
Identification of domains from NMR structure bundles
CYTOSCAPE
Platform for visualizing molecular interaction networks and biological pathways and integrating networks with annotations
DANGLE
Predicts protein backbone angles and assignments of chemical shifts using a DB of known structures and shifts
DASHA
Process heteronuclear NMR relaxation data
dataChord Spectrum Analyst
NMR data processing and analysis software for big, small, and mixtures of molecules
dataChord Spectrum Miner
Integrated application for NMR metabolomics and spectrum mining
DATAWARRIOR
Data visualization and analysis program with embedded chemical intelligence
DEEP Picker
A deep neural network for accurate deconvolution of complex two-dimensional NMR spectra
DOSY Toolbox
For processing PFG-NMR diffusion data
drawnmr
Module for viewing NMR data in Python
DYNAMO
The NMR molecular dynamics and analysis system
EISD
Probability scores to ensembles of Intrinsically Disordered Proteins (IDPs) based on their fit to experimental data
ENSEMBLE
Tools to determine and analyze the weighted ensemble of structures in unfolded states
FANDAS 2.0
Tool to predict peaks in multidimensional NMR experiments on proteins
Farseer-NMR
A software suite for automatic treatment, analysis and plotting of large and multivariable datasets of bioNMR peaklists
FASTModelFree
Rapid automated analysis of solution NMR spin-relaxation data
FID-Net
Deep Neural Networks for Analysing NMR time domain data.
FitNMR
Open-source R package for extracting peak parameters
Flexible-meccano
A tool for the generation of explicit ensemble descriptions of intrinsically disordered proteins and their associated experimental observables
FoXS
FoXS is a method for computing a theoretical scattering profile of a structure and fitting of experimental profile
FuDA
Analyse nD NMR correlation spectra
Gctf
GPU accelerate real-time determination and correction of the contrast transfer function
Geometric-Approximation
Computational approach to characterize protein dynamics from adiabatic relaxation dispersion experiments
GISSMO
Efficient calculation and refinement of spin system matrices
GLOVE
Fit relaxation dispersion data and test exchange models
GNAT
A general tool for processing NMR data
GOAP
All-atom statistical potential for protein structure prediction
GREMLIN
Method to learn a statistical model of a protein family capturing conservation and co-evolution patterns
GROMACS
A versatile package to perform molecular dynamics
GUARDD
Organizes, automates, and enhances the analytical procedures which operate on CPMG RD data
HMMER
Hidden Markov models for sequence profile analysis
hmsIST
Estimate the spectrum for nonuniformly sampled data using iterative soft thresholding
HullRad
Algorithm for calculating hydrodynamic properties of a macro-molecule from a structure file
hydroNMR
Calculation of NMR relaxation parameters of small macromolecules from a PDB file
ICOSHIFT
Solves signal alignment problems in metabonomic NMR data analysis.
ImageJ-Fiji
Image processing distribution of ImageJ, bundling many plugins to facilitate image analysis
IMP
IMP provides an open source C++ and Python toolbox for solving complex modeling problems
InChI
InChI provides unique labels for well-defined chemical substances
INFOS
Tool for fitting complicated spectra to better quantify peak amplitudes, integrals, and positions
Jellyfish
Simulate and view NMR spectra of spin systems in the liquid state experiencing J-couplings
Jupyter
Allows you to create and share documents that contain live code, equations, visualizations and narrative text
KdCalc
Determines binding constants by fitting NMR titration data in the fast exchange regime
LarmorCa
Predicts protein backbone (HN, N, HA, CA, CB) chemical shifts from a PDB structure
LARMORD
Simple and efficient program for predicting non-exchangeable 1H and protonated 13C RNA chemical shifts
localCIDER
Calculates and presents various sequence parameters associated with disordered protein sequences
M2MTool
A software tool to facilitate depositing data to BMRB from within NMRbox.
MADByTE
Using 2D NMR to streamline Natural Product Research
MARS
Robust automatic backbone assignment of proteins even with extreme chemical shift degeneracy
MATLAB
Numerical computing environment
MATLAB Compiler Runtime
Run compiled MATLAB applications or components without installing MATLAB
MD2NOE
Direct NOE simulation from long MD trajectories
MDAnalysis
MDAnalysis is a Python library to analyze molecular dynamics trajectories
MddNMR
A program for processing of non-uniformly sampled multidimensional NMR spectra
MDTraj
Read, write and analyze MD trajectories with only a few lines of Python code
MESMER
Analyzes the experimentally averaged data obtained from any number of experimental techniques such as SAXS and NMR
MestReNova (Mnova)
A top class software suite to process your analytical chemistry data
MetaboAnalystR
An R package for comprehensive analysis of metabolomics data
Metabolomics toolbox
Metabolomics toolbox
MetScape
A bioinformatics framework for the visualization and interpretation of metabolomic and expression profiling data
MMTSB Toolset
A collection of perl-based utilities and libraries for multiscale protein structure modeling
Modelfree
Optimizing “Lipari-Szabo model free” parameters to heteronuclear relaxation data
MODELLER
Homology or comparative modeling of protein three-dimensional structures
Module2
Analyzes residual dipolar couplings and residual chemical shifts measured in partially aligned proteins and nucleic acids
mol2sphere
Convert a molecule into a set of spheres of variable radii for visualization and modeling
Mollib
Program and Python library for the validation, quality analysis and manipulation of molecular structures
MOLMOL
Molecular graphics program for displaying, analyzing, and manipulating biological macromolecules
MolProbity
All-atom structure validation for macromolecules
MoSART
To provide an easily extensible application for computing biomolecular structure from NMR data
MotionCor2
Corrects electron beam-induced sample motion
mTM-align
Efficient protein structure comparisons
MVAPACK
Tools for processing and analyzing chemometric data
NAMD
NAMD is computer software for molecular dynamics simulation, written using the Charm++ parallel programming model
NESSY
Analyse NMR relaxation dispersion data of either CPMG or R1p (R1rho) dispersion experiments
NESTA-NMR
Fast and accurate reconstruction of NUS data
nightshift
Python command line utility and library for plotting simulated 2D and 3D NMR spectra from assigned chemical shifts in the BMRB
NMRDraw
NMRDraw is the companion graphical interface for NMRPipe and its processing tools
NMRFAM-SPARKY
A graphical NMR assignment and integration program for proteins, nucleic acids, and other polymers
nmrfit
Quantitative NMR analysis through least-squares fit of spectroscopy data
NMRFx Analyst
Data processing program utilizing Python for scripts and a full Java based GUI
NMRFx Processor
Data processing program utilizing Python for scripts and a full Java based GUI
NMRFx Structure
Features for structure calculation and chemical shift prediction
nmrglue
A module for working with NMR data in Python
NmrLineGuru
A graphical user interface (GUI) based user-friendly tool to simulate and fit NMR line shapes with multi-state equilibrium models
NMRmix
A Tool for the Optimization of Compound Mixtures in 1D 1H NMR Ligand Affinity Screens
NMRPipe
Multidimensional spectral processing and analysis of NMR data
NMRPy
A Python module for processing NMR spectra
NMR-scripts
A collection of small scripts of various functions
nmrstarlib
A Python library that facilitates reading and writing NMR-STAR formatted files used by BMRB for archival of NMR data
NMRViewJ
The Application for Visualization and Analysis of Macromolecular NMR Software
nmr_wash
Suppression of artifacts in NMR spectra obtained from sparsely sampled data
NUScon
Workflow tool for running NUS reconstructions on challenge data in support of NUScon evaluation
nus-tool
Utility for generating and analyzing NUS sample schedules
Open Babel
A chemical toolbox designed to search, convert, modify, or analyze chemical files
OpenMM
A high performance toolkit for molecular simulation
OpenVnmrJ
Open source version of Varian's/Agilent's VnmrJ software
OSPREY
Suite of programs for computational structure-based protein design
PALES
Prediction of sterically induced alignment in a dilute liquid crystalline phase
PANAV
PANAV is a Java based structure-independent chemical shift validation and re-referencing tool
ParmEd
A tool for aiding in investigations of biomolecular systems using molecular simulation packages (Amber, CHARMM, and OpenMM)
PATI
Predicts the alignment tensor and RDC's under steric alignment
PDBStat
NMR restraint analysis software and converter
pdb-tools
A swiss army knife for manipulating and editing PDB files.
PAL
A library of programs to assist in peak assignment and validation
PEAKY
Peak detection in NMR spectra for 1D to 4D spectra
PINT
A user-friendly software for rapid and accurate analysis of NMR spectra
PLUMED
The community-developed PLUgin for MolEcular Dynamics
PLUQ
Predict amino acid residue types and secondary structure assignments from chemical shifts
POISSON-GENERATOR
Generates NUS Poisson Gap sample schedules
POMONA
Chemical shift guided protein structure alignment
PONDEROSA
Software package for automated protein 3D structure determination
POOL
Suite of programs for protein loop backbone structure determination using RDCs
PPM/PPM_ONE
Chemical shift prediction for a single structure (PPM_One) or to account for motional averaging to molecular ensembles, such as MD simulations
Probe
Evaluates atomic packing by generating “contact dots” where atoms are in close proximity
PROCHECK
Checks the stereochemical quality of a protein structure
PROMEGA
Proline Omega angle prediction from sequence and chemical shifts
PROTEIN-DYNAMICS
Predict NH and methyl order parameters from structure
py4xs
py4xs: a python package for processing x-ray scattering data
pyIPINE
Python script for submitting and retrieving an I-PINE job
PyMOL
A molecular visualization system on an open source foundation, maintained and distributed by Schrödinger
PyNMR-STAR
A Python module for reading, writing, and manipulating NMR-STAR files
PyShifts
A PyMOL plugin for assessing the global quality of RNA structures using NMR chemical shifts
Qhull
Computes the convex hull of a shape, such as a protein
QSched
Quantile-directed nonuniform sampling
RASMOL
Molecular Graphics Visualisation Tool
RASPnmr
Uses structure-based chemical shift predictions to solve the backbone resonance assignment problem
raw
Processing and analysis of Small Angle X-ray Scattering (SAXS) data
RCI
Predict protein flexibility using secondary chemical shifts
RCS
A program for computing NMR aromatic ring current shifts
RDC-PANDA/Analytic
Programs for NOE assignment and structure determination starting with a global fold calculated from exact solutions to the RDC equations
REDCAT
The analysis of residual dipolar couplings (RDCs) for structure validation and elucidation
REDCRAFT
Tool for determining a protein's structure using residual dipolar couplings (RDCs)
Reduce
A program for adding hydrogens to a PDB molecular structure file
relax
Analysis software for Model-free, NMR relaxation (R1, R2, NOE), reduced spectral density mapping, relaxation dispersion
RELION
Empirical Bayesian approach to refinement of 3D reconstructions or 2D class averages in CryoEM
Remediator
Converts PDB files between PDBv2.3 and PDBv3.2 formats in either direction
RESMAP
Computes the local resolution of 3D density maps studied in structural biology, primarily in CryoEM
Ring NMR Dynamics
Characterization of protein and nucleic acid conformational dynamics and kinetics using solution and solid-state NMR
RNAstructure
RNAstructure is a complete package for RNA and DNA secondary structure prediction and analysis
rNMR
Visualizing and interpreting one and two dimensional NMR data
RNMRTK
General-purpose NMR data processing package, including maximum entropy spectral reconstruction
Rosetta
A software suite of algorithms for computational modeling and analysis of protein structures
ROTDIF3
Determines the overall rotational diffusion tensor from spin-relaxation data
RUNER
Enables seamless modifications of atom force field parameters in the molecular modeling software package Xplor-NIH
SEER
Program for the reconstruction of non-uniformly sampled NMR data
SES
Recovers a representative conformational ensemble from underdetermined RDC data
SHIFTS
Computes proton chemical shifts from empirical formulas
ShiftX
Predicts 1H, 13C and 15N chemical shifts for your favorite protein
SHIFTX2
Predicts both the backbone and side chain 1H, 13C and 15N chemical shifts for proteins
SHIMpanzee
A program for the simulation of NMR shim lineshapes
SIMPSON
General-purpose software package for simulating virtually all kinds of solid-state NMR experiments
SMILE
Algorithm to integrate a priori information about NMR signals for reconstruction of non-uniformly sampled (NUS) multidimensional data
SPARTA+
Neural network algorithm to make rapid chemical shift prediction on the basis of known structure
CONNJUR Spectrum Translator
CONNJUR Spectrum Translator is a free, extensible, and open source application for NMR File Spectral Format Conversion
Spinach
Spinach is a fast spin dynamics simulation library
SpinDrops
An interactive quantum spin simulator that uses the DROPS Representation
ssNake
Versatile tool for processing and analysing NMR spectra
SSP
Secondary structure propensities from chemical shifts and 13C chemical shift referencing
STARXML
XML to and from NMR-STAR converter
STRIDE
Protein secondary structure assignment from atomic coordinates
TALOS+
Prediction of protein backbone torsion angles from NMR chemical shifts
TALOS-N
Prediction of protein backbone and sidechain torsion angles from NMR chemical shifts
tameNMR
Suite of tools for processing and analysis of NMR data from metabolomics experiments
taurenmd
A command-line interface for analysis routines of Molecular Dynamics data
Tensor2
NMR Relaxation analysis of internal motions using the Lipari-Szabo or extended Lipari-Szabo method
TensorView
A software tool for displaying NMR tensors
tiger
A periodic table with detailed information on their NMR properties
TITAN
2D NMR lineshape analysis to monitor protein-ligand interactions
TopSpin
Bruker's software package for NMR data processing and analysis
TreeView
Gene Expression Visualization Tool
TreeView3
Java app for visualizing large data matrices. It can load a dataset, cluster it, browse it, customize its appearance and export it into a figure.
TREND
Resolve trends of change in imaging, spectra, or other data with ease
UCBShift
Predict chemical shifts for backbone atoms and β-carbon of a protein in solution using machine learning
Unblur
Aligns the frames of movies recorded on an EM to reduce image blurring due to beam-induced motion
VMD
VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems
VMD-XPLOR
Combination of the X-PLOR structure determination program and VMD Visual Molecular Dynamics
Wattos
Programs to analyze, annotate, parse, and disseminate NMR data
WHAT IF
Versatile molecular modelling package that is specialized on working with proteins and the molecules in their environment
XDrawChem
Molecule drawing program
XEASY
Interactive, computer-supported NMR spectrum analysis
Xipp
NMR analysis software for biomolecules
Xplor-NIH
A structure determination program which builds on the X-PLOR program
XSSP
A series of PDB-related databanks for everyday needs
xyza2pipe
Cross conversion environment of higher dimensional NMR spectra in several different formats