Popular GitHub Repositories for Molecules

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

Tensorflow + Molecules = TensorMol

Implementation of the Equiformer, SE3/E3 equivariant attention network that reaches new SOTA, and adopted for use by EquiFold for protein folding

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

Graph convolutions in Keras with TensorFlow, PyTorch or Jax.

Pytorch reimplementation of Molecule Attention Transformer, which uses a transformer to tackle the graph-like structure of molecules

Auto-regressive causal language model for molecule (SMILES) and reaction template (SMARTS) generation based on the Hugging Face implementation of OpenAI's GPT-2 transformer decoder model

Deep Learning And Applied Artificial Intelligence Project 2019/2020 - Molecular Synthesis & Reconstruction

Mapping properties to molecules in QM7-X

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

Score-Based Generative Model for Molecules

Master thesis: JAT (Jraph Attention Networks), a deep learning architecture to predict the potential energy and forces of molecules. Adapts Graph Attention Networks (GATv2) within the Message Passing Neural Networks framework to computational chemistry in JAX

SPQR (Streaming Product QuantIzation for moleculaR data): Streaming Product Quantization (PQ) for large-scale clustering of molecular data (or other high-dimensional data) to form approximate clustering in a streaming fashion, without requiring all data to be in memory at once