entity-trajectory

PyRod - Tracing water molecules in molecular dynamics simulations

MD pharmacophores and virtual screening

End-To-End Molecular Dynamics (MD) Engine using PyTorch

Toolbox for molecular animations in Blender, powered by Geometry Nodes.

Solvation Structure and Thermodynamic Mapping

Public development project of the LAMMPS MD software package

A pocket volume analyzer for use in protein modeling.

🏗️ Statistical models for biomolecular dynamics 🏗️

WebGL protein viewer

Detect and characterize binding pockets from molecular simulations.

OpenMM is a toolkit for molecular simulation using high performance GPU code.

Differentiable, Hardware Accelerated, Molecular Dynamics

🚂 Python API for Emma's Markov Model Algorithms 🚂

A comprehensive macromolecular library

gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files.

OpenMM plugin to define forces with neural networks

Dynamic pharmacophore modeling of molecular interactions

Fast and All atom Protein-Ligand Interaction Profiler

Powerful, efficient particle trajectory analysis in scientific Python.

Library for computing dynamic non-covalent contact networks in proteins throughout MD Simulation