Software Registry

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.

ALATIS

A tool for assigning unique and reproducible labels to all atoms of small molecules

almost

All atom molecular simulation toolkit.

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

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

AutoAssign

Automating the analysis of backbone resonance assignments.

Azara

A suite of programs to process and view NMR data.

BATMAN

An R package for estimating metabolite concentrations from Nuclear Magnetic Resonance spectral data using a specialised MCMC algorithm

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.

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.

CH3Shift

Structure-based prediction of protein methyl group chemical shifts.

CHEMEX

Fit chemical exchange induced shift and relaxation data.

CLUSTAL W/X

Multiple alignment of nucleic acid and protein sequences

CNS

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_ST

CONNJUR_ST is a free, extensible, and open source application for NMR File Spectral Format Conversion.

CPMG-Fit

Fits CPMG relaxation dispersion data for analysis of chemical exchange in NMR spectroscopy.

CPMGFit

Fits CPMG relaxation dispersion data for analysis of chemical exchange in NMR spectroscopy.

CS-GAMDy

A robust algorithm for refining protein structures with NMR chemical shifts.

CS-Rosetta (BMRB)

Submission tool for sending jobs to the BMRB CS-Rosetta server.

CSCDP

Chemical shift calculation for chemically denatured proteins.

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

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

FASTModelFree

Rapid automated analysis of solution NMR spin-relaxation data.

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

hmsIST

Estimate the spectrum for nonuniformly sampled using iterative soft thresholding.

HullRad

Algorithm for calculating hydrodynamic properties of a macro-molecule from a structure file

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.

Jellyfish

Simulated 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

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.

MESMER

Analyzes the experimentally averaged data obtained from any number of experimental techniques such as SAXS and NMR

MetaboAnalystR

An R package for comprehensive analysis of metabolomics data

MetScape

A bioinformatics framework for the visualization and interpretation of metabolomic and expression profiling data

MMTSB

A collection of perl-based utilities and libraries for multiscale protein structure modeling

Mnova

A top class software suite to process your analytical chemistry data

ModelFree

Optimizing "Lipari-Szabo model free" parameters to heteronuclear relaxation data.

MODELLER

Homology or comparative modeling of protein three-dimensional structures.

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 bean-induced sample motion

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.

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.

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.

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.

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.

nus-tool

Utility for generating, converting, 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)

PINT

A user-friendly software for rapid and accurate analysis of NMR spectra

PLUQ

Predict amino acid residue types and secondary structure assignments from chemical shifts.

PONDEROSA

Software package for automated protein 3D structure determination.

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

PROMEGA

Proline Omega angle prediction from sequence and chemical shifts.

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

RASMOL

Molecular Graphics Visualisation Tool.

raw

Processing and analysis of Small Angle X-ray Scattering (SAXS) data.

RCI

Predict protein flexibility using secondary chemical 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).

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

RESMAP

Computes the local resolution of 3D density maps studied in structural biology, primarily in CryoEM

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.

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

SHIFTS

Computes proton chemical shifts from empirical formulas.

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 simulation 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.

SpinDrops

An interactive quantum spin simulator that uses the DROPS Representation

SQLite

A self-contained, serverless, zero-configuration, transactional SQL database engine.

ssNake

Versatile tool for processing and analysing NMR spectra

SSP

Secondary structure propensities from chemical shifts and 13C chemical shift referencing.

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

tiger

A periodic table with detailed information on their NMR properties

TITAN

2D NMR lineshape analysis to monitor protein-ligand interactions

TREND

Resolve trends of change in imaging, spectra, or other data with ease.

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

This package allows manual manipulation of the protein structures to satisfy experimental NMR data

XDrawChem

Molecule drawing program.

XEASY

Interactive, computer-supported NMR spectrum analysis.

Xplor-NIH

A structure determination program which builds on the X-PLOR program.

xyza2pipe

Cross conversion environment of higher dimensional NMR spectra in several different formats

YesWorkflow

A user-oriented, language-independent tool for recovering workflow information from scripts.