torchdrug

Model molecules and proteins for property prediction and generation with PyTorch and RDKit.

Updated May 10, 2026
One-click install
npx skills add https://github.com/Imad-Oute/ResearchForge --skill torchdrug-imad-oute
Or copy as Structured Prompt for Agent
Please help me install this Agent Skill.
Skill: torchdrug
Source: https://github.com/Imad-Oute/ResearchForge/tree/main/OpenSource-Projects/claude-scientific-skills/scientific-skills/torchdrug
Command: npx skills add https://github.com/Imad-Oute/ResearchForge --skill torchdrug-imad-oute

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires torch, rdkit, sklearn, numpy, and includes scripts (resource) and references (resource) components.

What problem does it solve?

TorchDrug addresses the need for an integrated platform that simplifies and accelerates research in drug discovery, molecular science, and protein analysis by providing modular tools for data handling, modeling, and prediction.

Core Features & Use Cases

  • Molecular Property Prediction: Predict biological and chemical properties of molecules including toxicity, solubility, and activity.
  • Protein Modeling: Analyze protein sequences and structures for function, stability, and interactions.
  • Knowledge Graph Reasoning: Complete and analyze biomedical knowledge graphs for link prediction and discovery.
  • Molecular Generation & Retrosynthesis: Generate novel molecules and plan synthetic routes to facilitate drug design.
  • Model Flexibility: Supports various architectures like GNNs, transformers, and flow-based models, adaptable to different data types and research goals.

Quick Start

Load a molecular dataset and train a graph neural network to predict chemical properties in a single, straightforward command.

Frequently Asked Questions about torchdrug

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I predict molecular properties like toxicity and solubility using graph neural networks?

To predict molecular properties like toxicity and solubility, you can load a molecular dataset and train a graph neural network within a unified framework. This process requires PyTorch and RDKit for data processing and model training.

What's the best way to plan synthetic routes for novel drug discovery?

The best way to plan synthetic routes for drug discovery involves using generative models for molecular generation and retrosynthesis. This toolkit supports generating novel molecules and planning synthetic routes to facilitate drug design.

Can I analyze protein sequences and structures for function and stability in PyTorch?

Yes, you can analyze protein sequences and structures for function, stability, and interactions in PyTorch. The platform provides an extensive suite of tools specifically designed for protein modeling within its unified framework.

How does knowledge graph reasoning work for biomedical link prediction?

Knowledge graph reasoning for biomedical link prediction works by completing and analyzing biomedical knowledge graphs. The system uses graph-based architectures to perform link prediction and discovery for complex scientific research scenarios.

Do I need RDKit and sklearn installed to perform molecular modeling?

Yes, you need RDKit and sklearn installed alongside PyTorch and numpy to perform molecular modeling. These core libraries are required dependencies for handling data processing and training models across various molecular and protein workflows.

What architectures are supported for generative tasks in molecular science?

Supported architectures for generative tasks in molecular science include graph neural networks (GNNs), transformers, and flow-based models. This model flexibility allows adaptation to different data types and research goals.