Reverse Dependencies of MDAnalysis

The following projects have a declared dependency on MDAnalysis:

• ai2-kit — no summary
• arctic3d — Automatic Retrieval and ClusTering of Interfaces in Complexes from 3D structural information
• BFEE2 — Binding Free Energy Estimator 2
• biobb-cmip — biobb_cmip is the Biobb module collection to compute classical molecular interaction potentials.
• bioen — Bayesian Inference Of ENsembles
• buildh — Build hydrogen atoms from united-atom molecular dynamics of lipids and calculate the order parameters.
• catflow — Analyzing tool for deep learning based chemical research.
• cleanup-sims — Cleans up your messy Gromacs simulations
• CodeEntropy — CodeEntropy tool with POSEIDON code integrated to form a complete and generally applicable set of tools for computing entropy of macromolecular systems from the forces sampled in a MD simulation.
• colvars-finder — Find collective variables (CVs) by training neural networks.
• correlationPlus — A Python package to calculate, visualize and analyze correlations of proteins.
• cpctools — A package for analysing molecular systems
• dcdftbmd-tools — A Toolkit for handling DCDFTBMD input/output
• deepdrivemd — Deep-Learning Driven Adaptive Molecular Simulations
• DEERPREdict — A package for DEER and PRE predictions based on molecular dynamics ensembles. Can be installed with pip.
• dmol-book — Style and Imports for dmol Book
• docking-eval — Evaluates docking poses based on the CAPRI criteria
• DRSIP — DRSIP docking package
• dylightful — Package to uncover hidden interaction patterns in supramolecular complexes
• dynAMMo — dynAMMo – dynamic Augmented Markov Models
• dynetan — A Python implementation for Dynamical Network Analysis.
• ectoolkits — Small Package to Postprocessing Results
• encodermap — python library for dimensionality reduction
• ENPMDA — parallel analysis for ensemble simulations
• evodiff — Python package for generation of protein sequences and evolutionary alignments via discrete diffusion models
• FRETpredict — A package for FRET Efficiency prediction of protein structures and trajectories, based on the Rotamer Library Approach (RLA). Can be installed with pip.
• gamdvdr — Variable Density Reweighting for GaMD Simulations
• gemdat — Generalized Molecular Dynamics Analysis Tool
• genice2-mdanalysis — A GenIce format plugin to make a Universe of MDAnalysis.
• grsq — Structure factor and X-ray scattering from radial distribution functions
• HyresRebuilder — Rebuild atomistic model from HyRes model.
• kimmdy — Kinetic Monte Carlo Molecular Dynamics
• kimmdy-grappa — Parameterization interface between KIMMDY and GrAPPa
• kimmdy-reactions — Reaction template for KIMMDY
• kinisi — Efficient estimation of diffusion processes from molecular dynamics.
• kperm — Toolkit for Analysis of Permeation Cycles in Potassium Channels
• lipyphilic — Analyse MD simulations of lipids with python'
• locuaz — Antibody optimization protocol
• macchiato — Data-driven nearest neighbor models for predicting experimental results on silicon lithium-ion battery anodes.
• maicos — Analyse molecular dynamics simulations of interfacial and confined systems.
• md2stl — Python tools to convert a MD simulation file into a .stl file ready to be 3d printed.
• mda-tui — A textual user interface (TUI) for MDAnalysis
• mdacli — A command line client for MDAnalysis Analysis classes.
• mdaencore — Ensemble overlap comparison software for molecular data.
• mdahole2 — A Python interface for the HOLE suite tools to analyze an ion channel pore or transporter pathway as a function of time or arbitrary order parameters.
• mdakit-sasa — This kit allows the calculation of a solvent-accessible-surface area of a trajectory
• mdapackmol — An MDAnalysis wrapper around Packmol
• mdapackmol-fmt — An MDAnalysis wrapper around Packmol
• MDContentAnalysis — Package for analysing content of protein channels/tunnel in molecular dynamics simulations. Analyses trajectories. Built upon MDAnalysis, and uses Hole 2.0 or Mole 2.5
• MDCraft — A batteries-included toolkit of analysis modules and helper functions
• mdgo — A codebase for MD simulation setup and results analysis.
• mdhelper — A batteries-included toolkit of analysis modules and helper functions
• mdigest — Best practices made easy for analysis of correlated motions from molecular dynamics simulations.
• mdml — Application of Deep learning on molecular dymanamics trajectories
• mdorado — Collection of scripts to analyse molecular dynamics simulations.
• MDPOW — A library for computing solvation/water partitioning coefficients using molecular dynamics simulations
• mdsimseval — Collective analysis on a set of Molecular Dynamics simulations.
• mdsubsampler — no summary
• mdsynthesis — a persistence engine for molecular dynamics data
• mdvoxelsegmentation — Leaflet segmentation of lipids or other amphipathic molecules of olecular dynamics stuctures and trajectories.
• membrane-curvature — MDAnalysis tool to calculate membrane curvature from MD simulations.
• memgen — Calls MemGen service located at http://memgen.uni-saarland.de/api
• metallicious — no summary
• miko-analyzer — Analyzing tool for deep learning based chemical research.
• molann — "PyTorch Artificial Neural Networks (ANNs) for Molecular Systems",
• molgri — Generate molecular pseudotrajectories based on rotational grids.
• MolPainter — Tool for drawing complex planar molecular systems of arbitrary composition and molecule placement
• MolPainter-gpantel — Tool for drawing complex planar molecular systems of arbitrary composition and molecule placement
• nmrformd — Calculate dipolar NMR relaxation time from molecular dynamics trajectory file
• nmrgnn-data — Chemical shift prediction dataset
• OpenABC — no summary
• openmm-mdanalysis-reporter — MDAnalysis based reporter for OpenMM
• opennucleome — no summary
• pathsimanalysis — Calculates the geometric similarity of molecular dynamics trajectories using path metrics such as the Hausdorff and Fréchet distances.
• pcaviz-durrantlab — A script to compress molecular dynamics simulations so they can be visualized with PCAViz in a web browser.
• pcmap — Computing contact map for protein structures
• pensa — exploratory analysis and comparison of biomolecular conformational ensembles.
• pmda — Parallel Molecular Dynamics Analysis tools
• PoreFinding — PoreFinding package based on HOLE and MDAnalysis
• potsim2 — no summary
• prolif — Interaction Fingerprints for protein-ligand complexes and more
• prolint2 — ProLint2: Lipid-Protein Interaction Analysis.
• propkatraj — obtain pKas for titreatable residues from a simulation trajectory
• proteinflow — Versatile pipeline for processing protein structure data for deep learning applications.
• pypoc — Python package for analysis of molecular dynamics simulations of lipid membranes.
• QMzyme — QM-based enzyme model generation and validation.
• RCBS.py — Python package useful for analysing MD trajectories and creating QM/MM models built on top of MDAnalysis. All MD formats compatible with MDAnalysis are compatible with RCBS, while QM/MM capacities are compatible with ChemShell. The aim of this package is to develop an easy-to-use way to analyse MD trajectories, while keeping a good performance.
• RotamerConvolveMD — Analysis of spin label distances over structural ensembles
• sbmlcore — Constructs core features table for the application to machine learning models
• simlify — Simplify your molecular simulation workflow.
• simulariumio — Simularium Conversion helps convert simulation outputs to the format consumed by the Simularium viewer.
• SINATRA-Pro — Python3 package for SINATRA Pro.
• solvation-analysis — no summary
• sphericalHarmonicDecomposition — no summary
• supramolecular-sugar — SUpramolecular recoGnition prediction in porous moleculAR materials
• swarm-cg — Tools for automatic parametrization of bonded terms in coarse-grained molecular models, with respect to an all-atom trajectory
• taurenmd — A command-line interface for analysis routines in Molecular Dynamics data.
• ternviz — Render SMILES into 3D video
• transport-analysis — A Python package to compute and analyze transport properties.
• tripp — Trajectory Iterative pKa Predictor