Working with molecular structures in pandas DataFrames

EquiBind: geometric deep learning for fast predictions of the 3D structure in which a small molecule binds to a protein

Molecular Processing Made Easy.

Curses based ASCII molecule viewer for terminals.

overview of datasets for ML in chemistry

Official implementation of All Atom Diffusion Transformers (ICML 2025)

Radient turns many data types (not just text) into vectors for similarity search, RAG, regression analysis, and more.

Implementation of Torsional Diffusion for Molecular Conformer Generation (NeurIPS 2022)

Tensorflow + Molecules = TensorMol

Source code for GNN-LSPE (Graph Neural Networks with Learnable Structural and Positional Representations), ICLR 2022

ScaffoldGraph is an open-source cheminformatics library, built using RDKit and NetworkX, for the generation and analysis of scaffold networks and scaffold trees.

A tensorflow.keras generative neural network for de novo drug design, first-authored in Nature Machine Intelligence while working at AstraZeneca.

Making self-supervised learning work on molecules by using their 3D geometry to pre-train GNNs. Implemented in DGL and Pytorch Geometric.

A collection of resources for Deep Learning in Python for Life Sciences (with focus on biotech and pharma).

A short and easy PyTorch implementation of E(n) Equivariant Graph Neural Networks

Geom3D: Geometric Modeling on 3D Structures, NeurIPS 2023

Graph convolutions in Keras with TensorFlow, PyTorch or Jax.

Python macromolecular parsing (with .pdb/.cif/.mmtf parsing and production)

Monte Carlo and Molecular Dynamics Simulation Package

🌟 [NeurIPS '25 Spotlight] Fair and transparent benchmark of machine learning interatomic potentials (MLIPs), beyond basic error metrics https://openreview.net/forum?id=SAT0KPA5UO

The official PyTorch implementation of "Pathfinder Discovery Networks for Neural Message Passing" (WebConf '21)

Learning Graph Models for Retrosynthesis Prediction (NeurIPS 2021)

D3 based interactive visualization library + tool to make render atoms and molecules learning chemical bonding in a fun way.

A fragment-based molecular assembly toolkit

An enterprise react-native template application showcasing - Testing strategy, Global state management, middleware support, a network layer, component library integration, localization, navigation configuration and CI

A 3D first person serious game, aiming to teach player about molecules through an immersive and fun way.

A cross-platform application for visualization of molecular databases.

Streamlit Component for creating Speck molecular structures within Streamlit Web app.

Reagent prediction with Molecular Transformer. Improvement of data for reaction product prediction in a self-supervised fashion.

Molecular Reinforcement Learning with Adaptive Intrinsic Reward for Goal-directed Molecular Generation.