Registry of MDAnalysis Toolkits (MDAKits)

The MDAKit registry contains a list of all MDAKits which have been added to this repository. The aim of this registry is to:

1. Inform members of the community about existing MDAKits

2. Provide sufficient details to allow others to use and potentially participate in the development of the MDAKits

3. Provide information about the current state of the MDAKits and how they interact with the latest versions of MDAnalysis

Each of the MDAKits in the following table links to a page with more details about what the MDAKits do, how they can be installed and how to participate in their development.

List of registered MDAKits

MDAKit	Keywords	Authors	CI badges
maicos	Molecular Dynamics, Confined Systems	maicos authors
QMzyme	theozyme, compuzyme, cluster, active-site, biocatalysis, enzyme-mechanisms, quantum-mechanics, QM-input	QMzyme authors
MDonatello	2D, visualization, jupyter notebook, ipywidgets, rdkit, display	MDonatello authors
qvalue	Q value, Native Contacts	qvalue authors
zenowrapper	hydrodynamic, hydrodynamic radius, diffusion coefficient, intrinsic viscosity, sedimentation coefficient, electric polarizability, monte carlo, walk-on-spheres	Jennifer A Clark, Derek Juba, Walid Keyrouz, Debra Audus, Jack Douglas
MDANCE	clustering, machine-learning, algorithms, molecular-dynamics, protein-refinement	MDANCE authors
twodanalysis	Lipids, Lipids order parameters, 2D projections, Lipid metrics, Lipid study, Biopolymers, Proteins, Membrane, RNA	twodanalysis authors
propkatraj	pKa, protein	propkatraj authors
packing_defect	MDAnalysis, membrane, protein, packing defects, lipids, molecular dynamics	Jay Braun Jr.
mdahole2	pores, ion channels, transporters, HOLE	mdahole2 authors
solvation-analysis	chemistry, electrolytes, solvation structure	orionarcher, hmacdope, laurlee, IAlibay
mda-tui	transformations, TUI	mda-tui authors
mdakit-sasa	SASA, FreeSASA, ShrakeRupley, LeeRichards	mdakit-sasa authors
pytim	Surface analysis, Intrinsic properties	pytim authors
mdaencore	ensemble, similarity, covariance, PCA	mdaencore authors
OpenMMDL	MD simulations, Protein-ligand analysis, flask-based webserver, visualization, openmm, rdkit, nglview	OpenMMDL authors
openmm-mdanalysis-reporter	OpenMM, Reporters	openmm-mdanalysis-reporter authors
membrane-curvature	membranes, curvature, molecular dynamics	membrane-curvature authors
transport-analysis	transport properties, molecular dynamics	transport-analysis authors
mdacli	command line interface, molecular-dynamics	mdacli authors
zarrtraj	streaming, trajectory, zarr, h5md, hdf5, AWS S3 Buckets, Google Cloud Buckets, Azure Blob Storage, Azure Data Lake	zarrtraj authors
lipyds	lipids, membranes	lilyminium
mdachecker	structure analysis, conformation checks	IAlibay
ProLIF	drug-design, cheminformatics, molecular-dynamics	Cédric Bouysset
Menger_Curvature	IDP, IDR, flexibility, Menger curvature, protein	Menger_Curvature authors
waterdynamics	water, hydrogenbonds, MSD	waterdynamics authors
spyrmsdkit	spyrmsd, RMSD, symmetry-corrected RMSD, drug discovery	spyrmsdkit authors
helanal	protein, structure, helix	helanal authors
PathSimAnalysis	similarity, paths, metrics	PathSimAnalysis authors
lipidorderkit	Lipids, Lipids order parameters, SCD, Lipid metrics, Lipid study	lipidorderkit authors
domhmm	membranes, molecular dynamics, nanodomains, microdomains, machine learning	domhmm authors