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torchdrug

PyTorch-native graph neural networks for molecules and proteins. Use when building custom GNN architectures for drug discovery, protein modeling, or knowledge graph reasoning. Best for custom model development, protein property prediction, retrosynthesis. For pre-trained models and diverse featurizers use deepchem; for benchmark datasets use pytdc.

backend/cli/skills/chemistry/torchdrug/SKILL.md

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Nov 7, 2026
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# TorchDrug

## Overview

TorchDrug is a comprehensive PyTorch-based machine learning toolbox for drug discovery and molecular science. Apply graph neural networks, pre-trained models, and task definitions to molecules, proteins, and biological knowledge graphs, including molecular property prediction, protein modeling, knowledge graph reasoning, molecular generation, retrosynthesis planning, with 40+ curated datasets and 20+ model architectures.

## When to Use This Skill

This skill should be used when working with:

**Data Types:**
- SMILES strings or molecular structures
- Protein sequences or 3D structures (PDB files)
- Chemical reactions and retrosynthesis