Meeko

AutoDock Vina — fast open-source molecular docking engine for predicting protein-ligand binding poses and affinities. Uses gradient-optimization conformational search with Vina, Vinardo, or AutoDock4

1 shared topic • 2 shared operations

DiffDock — diffusion generative model for molecular docking that predicts protein-ligand binding poses. Uses a diffusion process over translations, rotations, and torsion angles to generate and rank d

1 shared topic • 2 shared operations

Gnina — deep learning molecular docking program built on AutoDock Vina. Uses convolutional neural networks (CNNs) to rescore protein-ligand poses for improved binding pose prediction and virtual scree

1 shared topic • 2 shared operations

MDAnalysis — Python library for analyzing molecular dynamics trajectories and atomic coordinate data. Supports 40+ file formats (DCD, XTC, TRR, PDB, GRO, AMBER, LAMMPS). Provides RMSD, RMSF, hydrogen

3 shared operations

MDTraj — Python library for reading, writing, and analyzing molecular dynamics trajectories. Supports 20+ formats (DCD, XTC, TRR, PDB, HDF5, NetCDF, etc.) with NumPy-native arrays. Provides RMSD, RMSF

3 shared operations