domain-molecular-simulation

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

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

SchNetPack - Deep Neural Networks for Atomistic Systems

NequIP is a code for building E(3)-equivariant interatomic potentials

Molsystem provides a general class for handling molecular and periodic systems

Force fields produced by the Open Force Field Initiative

MD pharmacophores and virtual screening

Detect and characterize binding pockets from molecular simulations.

An automated framework for generating optimized partial charges for molecules

Differentiable, Hardware Accelerated, Molecular Dynamics

A pocket volume analyzer for use in protein modeling.

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

MoleculeKit: Your favorite molecule manipulation kit

Standalone charge assignment from Espaloma framework.

An open library for the analysis of molecular dynamics trajectories

MDAnalysis is a Python library to analyze molecular dynamics simulations.

The Open Forcefield Toolkit provides implementations of the SMIRNOFF format, parameterization engine, and other tools. Documentation available at http://open-forcefield-toolkit.readthedocs.io

🚂 Python API for Emma's Markov Model Algorithms 🚂

Experiments with expanded ensembles to explore chemical space

OpenFF NAGL