lilyminium

cryojax

Cryo electron microscopy image simulation and analysis built on JAX.

best-of-atomistic-machine-learning

🏆 A ranked list of awesome atomistic machine learning projects ⚛️🧬💎.

stormm

yammbs

Internal tool for benchmarking force fields

tico

Torch-based internal coordinate geometry optimization

quacc

quacc is a flexible platform for computational materials science and quantum chemistry that is built for the big data era.

FriendsDontLetFriends

Friends don't let friends make certain types of data visualization - What are they and why are they bad.

molesp

Generate and visualize the ESP at the surface of a molecule

graphium

Graphium: Scaling molecular GNNs to infinity.

femto

A comprehensive toolkit for predicting free energies

NNPOps

High-performance operations for neural network potentials

smee

Differentiably evaluate energies using SMIRNOFF force fields

TDC

Therapeutics Commons (TDC-2): Multimodal Foundation for Therapeutic Science

cinnabar

Package for consistent reporting of relative free energy results

espaloma

Extensible Surrogate Potential of Ab initio Learned and Optimized by Message-passing Algorithm 🍹https://arxiv.org/abs/2010.01196

pyo3

Rust bindings for the Python interpreter

mdtraj

An open library for the analysis of molecular dynamics trajectories

torchmd-net

Training neural network potentials

pdb2pqr

PDB2PQR - determining titration states, adding missing atoms, and assigning charges/radii to biomolecules.

geomeTRIC

Geometry optimization code that includes the TRIC coordinate system

perses

Experiments with expanded ensembles to explore chemical space

ElementEmbeddings

Python package to interact with high-dimensional representations of the chemical elements

asapdiscovery

Toolkit for open antiviral drug discovery by the ASAP Discovery Consortium

academicpages.github.io

Github Pages template for academic personal websites, forked from mmistakes/minimal-mistakes

sage-2.2.0

Minor version of Sage line of force fields

pmx

Toolkit for free-energy calculation setup/analysis and biomolecular structure handling

openff-interchange

A project (and object) for storing, manipulating, and converting molecular mechanics data.

torchmd

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

glosario

A multilingual glossary for computing and data science terms.

private-gpt

Interact with your documents using the power of GPT, 100% privately, no data leaks