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.

Tensorflow + Molecules = TensorMol

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)

overview of datasets for ML in chemistry

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

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

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

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

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

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)

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

Monte Carlo and Molecular Dynamics Simulation Package

Avogadro is an advanced molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible rendering and a powerful plugin architecture.