domain-molecular-simulation

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

Force fields produced by the Open Force Field Initiative

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

Molsystem provides a general class for handling molecular and periodic systems

Differentiable, Hardware Accelerated, Molecular Dynamics

SchNetPack - Deep Neural Networks for Atomistic Systems

An automated framework for generating optimized partial charges for molecules

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

MD pharmacophores and virtual screening

Detect and characterize binding pockets from molecular simulations.

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

A pocket volume analyzer for use in protein modeling.

MolSysSuite

Public development project of the LAMMPS MD software package

🚂 Python API for Emma's Markov Model Algorithms 🚂

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

An open library for the analysis of molecular dynamics trajectories

MDAnalysis is a Python library to analyze molecular dynamics simulations.

Powerful, efficient particle trajectory analysis in scientific Python.

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