entity-trajectory

Cryptic binding pocket discovery from conformational ensembles. Open-source, reproducible, size-robust benchmarks against fpocket, PocketMiner and CryptoBench.

🏗️ Statistical models for biomolecular dynamics 🏗️

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

A pocket volume analyzer for use in protein modeling.

Solvation Structure and Thermodynamic Mapping

Detect and characterize binding pockets from molecular simulations.

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

Public development project of the LAMMPS MD software package

PyRod - Tracing water molecules in molecular dynamics simulations

WebGL protein viewer

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

MD pharmacophores and virtual screening

Differentiable, Hardware Accelerated, Molecular Dynamics

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

Powerful, efficient particle trajectory analysis in scientific Python.

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

An open library for the analysis of molecular dynamics trajectories

MDAnalysis is a Python library to analyze molecular dynamics simulations.

Fast and All atom Protein-Ligand Interaction Profiler