entity-trajectory

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

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

Public development project of the LAMMPS MD software package

MD pharmacophores and virtual screening

Detect and characterize binding pockets from molecular simulations.

🏗️ Statistical models for biomolecular dynamics 🏗️

PyRod - Tracing water molecules in molecular dynamics simulations

WebGL protein viewer

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

A pocket volume analyzer for use in protein modeling.

Solvation Structure and Thermodynamic Mapping

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

Differentiable, Hardware Accelerated, Molecular Dynamics

Powerful, efficient particle trajectory analysis in scientific Python.

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

Dynamic pharmacophore modeling of molecular interactions

Fast and All atom Protein-Ligand Interaction Profiler

A comprehensive macromolecular library

🚂 Python API for Emma's Markov Model Algorithms 🚂

OpenMM plugin to define forces with neural networks