entity-trajectory

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

Public development project of the LAMMPS MD software package

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

Solvation Structure and Thermodynamic Mapping

WebGL protein viewer

🏗️ Statistical models for biomolecular dynamics 🏗️

Detect and characterize binding pockets from molecular simulations.

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

A pocket volume analyzer for use in protein modeling.

MD pharmacophores and virtual screening

PyRod - Tracing water molecules in molecular dynamics simulations

Differentiable, Hardware Accelerated, Molecular Dynamics

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

A comprehensive macromolecular library

🚂 Python API for Emma's Markov Model Algorithms 🚂

An open library for the analysis of molecular dynamics trajectories

MDAnalysis is a Python library to analyze molecular dynamics simulations.

Dynamic pharmacophore modeling of molecular interactions

Fast and All atom Protein-Ligand Interaction Profiler

Powerful, efficient particle trajectory analysis in scientific Python.