Repository Index

Message Passing Neural Networks for Molecule Property Prediction

• machine-learning
• chemistry
• neural-networks
• drug-discovery

Molecular Sets (MOSES): A Benchmarking Platform for Molecular Generation Models

• machine-learning
• generative-models
• drug-discovery
• benchmark

Python package for graph neural networks in chemistry and biology

• deep-learning
• graph-neural-networks
• dgl
• cheminformatics

A PyTorch and TorchDrug based deep learning library for drug pair scoring. (KDD 2022)

• deep-learning
• pytorch
• deep-chemistry
• graph-neural-network

OpenChem: Deep Learning toolkit for Computational Chemistry and Drug Design Research

• computational-chemistry
• computational-biology
• deep-learning
• deep-neural-networks

Chainer Chemistry: A Library for Deep Learning in Biology and Chemistry

• deep-learning
• chemistry
• neural-network
• biology

Benchmarks for generative chemistry

A Euclidean diffusion model for structure-based drug design.

• ddpm
• drug-design
• equivariance
• generative-model

The official implementation of 3D Equivariant Diffusion for Target-Aware Molecule Generation and Affinity Prediction (ICLR 2023)

• ai-for-science
• diffusion-models
• drug-design
• equivariant-networks

GraphDTA: Predicting drug-target binding affinity with graph neural networks

Source code for "DeepDTA: deep drug-target binding affinity prediction"

• protein-ligand-interactions
• convolutional-neural-networks

a unified framework for modeling chemically reactive systems

• chemical-equilibrium
• chemical-kinetics
• reactive-transport
• chemical-reactions

A Python package for molecular docking with an extensive, highly-curated dataset and a set of realistic benchmark tasks for drug discovery.

Auto-QChem is an automated workflow for the generation and storage of DFT calculations for organic molecules.

• cheminformatics
• dft-calculations
• automation
• feature

The d-SEAMS C++ core engine

• molecular-dynamics-simulation
• molecular-dynamics
• trajectory-analysis
• lua

ChemMine Tools: open source web framework for small molecule analysis

Multi-stage Riemannian flow matching for physically valid molecular docking, with GNINA scoring, PoseBusters filtering, CLI inference, and benchmarks.

• alphafold3
• docking
• drug-design
• drug-discovery

UV-first benchmark for protein-ligand docking with reproducible annotation, pocket similarity, and HPC workflows.

• benchmark
• bioinformatics
• cheminformatics
• computational-chemistry

Accelerated similarity searching of small molecules (bioconductor package)