aravindprasad's Stars
MengwuXiao/GetBox-PyMOL-Plugin
A PyMOL Plugin for calculating docking box for LeDock, AutoDock and AutoDock Vina.
Valdes-Tresanco-MS/AMDock
(Linux and macOS) AMDock: Assisted molecular docking with AutoDock4 and AutoDockVina
m3g/packmol
Packmol - Initial configurations for molecular dynamics simulations
pablo-arantes/PythonDataScienceHandbook
Python Data Science Handbook: full text in Jupyter Notebooks
pablo-arantes/making-it-rain
Cloud-based molecular simulations for everyone
octavian-ganea/equidock_public
EquiDock: geometric deep learning for fast rigid 3D protein-protein docking
akiyamalab/MEGADOCK
An ultra-high-performance protein-protein docking for heterogeneous supercomputers
dansind/Placevent
Placevent - 3D-RISM-based solvent and ion placement software
drmaruyama/3D-RISM
jupyter-widgets-contrib/ipysheet
Jupyter handsontable integration
plotly/jupyter-dash
OBSOLETE - Dash v2.11+ has Jupyter support built in!
coleygroup/pyscreener
pythonic interface to virtual screening software
sokrypton/ColabFold
Making Protein folding accessible to all!
DrrDom/crem
CReM: chemically reasonable mutations framework
learningmatter-mit/geom
GEOM: Energy-annotated molecular conformations
openmm/pdbfixer
PDBFixer fixes problems in PDB files
mpcrlab/MolecularTransformerEmbeddings
Code and data for the Transformer neural network trained to translate between molecular text representations and create molecular embeddings.
chopralab/lemon
A framework for rapidly mining structural information from the Protein Data Bank
Grantlab/bio3d
A mirror of official bio3d development site at Bitbucket: https://bitbucket.org/Grantlab/bio3d. See also bio3d website: http://thegrantlab.org/bio3d
nglviewer/ngl
WebGL protein viewer
nglviewer/nglview
Jupyter widget to interactively view molecular structures and trajectories
maxscheurer/pycontact
Analysis of non-covalent interactions in MD trajectories
stanalyzer/ST-analyzer
Simulation Trajectory Analysis for Molecular Dynamics
RUBi-ZA/MD-TASK
Tool suite for analysing molecular dynamics trajectories using network analysis and PRS
eshamay/interfacemd
Tools for working with data from molecular dynamics simulations. Trajectory analysis, computational spectroscopy, density plots, distribution functions, atoms/molecules/systems - specializing in aqueous (water) systems made using Amber, Gromacs, and CP2K simulation packages.
matsunagalab/MDToolbox.jl
MDToolbox.jl: A Julia package for molecular dynamics trajectories analysis and modeling of biomolecules
harmsm/md-analysis-tools
scripts for analyzing molecular dynamics trajectories using VMD
ymatsunaga/mdtoolbox
MDToolbox: A MATLAB/Octave toolbox for statistical analysis of molecular dynamics trajectories
alanklam/MDEncoder
Python package for MD trajectory analysis using neural network
sizmailov/pyxmolpp2
Processing and analysis of MD trajectories