skills.rest
RamanEbrahimi
RamanEbrahimiCOMMUNITY
Explore all skills by this author →
WebsiteGitHub

torchdrug

Process molecular and protein data with graph neural networks for drug discovery tasks.

3|Updated Apr 17, 2026
Search Tags:#knowledge graph#drug discovery#graph neural networks#protein modeling#molecular property prediction
One-click install
npx skills add https://github.com/RamanEbrahimi/raman-marketplace --skill torchdrug-ramanebrahimi
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: torchdrug
Source: https://github.com/RamanEbrahimi/raman-marketplace/tree/main/plugins/agentic-research/skills/scientific-skills/torchdrug
Command: npx skills add https://github.com/RamanEbrahimi/raman-marketplace --skill torchdrug-ramanebrahimi

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires torch, torchdrug[full], rdkit, alphafold, and includes scripts (resource) and references (resource) and assets (resource) components.

What problem does it solve?

TorchDrug solves the problem of efficiently processing and analyzing complex molecular and protein data, enabling advanced tasks such as property prediction, protein modeling, and knowledge graph reasoning.

Core Features & Use Cases

  • Molecular Property Prediction: Predict chemical, physical, and biological properties of molecules from their structure.
  • Protein Modeling: Work with protein sequences, structures, and properties to predict function, structure, and interactions.
  • Knowledge Graph Reasoning: Predict missing links and relationships in biological knowledge graphs.
  • Molecular Generation: Generate novel molecular structures with desired properties.
  • Retrosynthesis: Predict synthetic routes from target molecules to starting materials.
  • Use Case: A researcher could use TorchDrug to predict the toxicity of a new drug candidate based on its molecular structure.

Quick Start

Run the following command to install TorchDrug:

uv pip install torchdrug

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 using graph neural networks in PyTorch?▼

Molecular property prediction is handled by constructing graph neural networks in PyTorch to process molecular structures and predict chemical, physical, and biological properties directly from the graph data.

Can I use RDKit and AlphaFold for protein modeling and knowledge graph reasoning?▼

Yes, protein modeling and knowledge graph reasoning rely on PyTorch alongside dependencies like RDKit for molecular structures and AlphaFold for protein sequences, structures, and function prediction.

What is the best way to predict missing links in biological knowledge graphs?▼

Knowledge graph reasoning predicts missing links and relationships in biological knowledge graphs by applying PyTorch-native graph neural networks to infer connections from existing graph data.

Do I need PyTorch to generate novel molecular structures with desired properties?▼

Yes, PyTorch is required as the foundational framework to run graph neural networks for molecular generation tasks, generating novel structures by learning from desired molecular properties.

How does retrosynthesis prediction work for identifying synthetic routes?▼

Retrosynthesis prediction works by using machine learning to map target molecules back to their starting materials, predicting viable synthetic routes through graph-based molecular analysis.

Can TorchDrug predict the toxicity of a new drug candidate based on its structure?▼

TorchDrug predicts the toxicity of new drug candidates by applying graph neural networks to analyze the structural representations of molecules and output biological property predictions.

Related Skills

Explore More Software Engineering Skills→
jackspacejackspace
16

torchdrug

Apply graph neural networks to drug discovery tasks with PyTorch.

Community
Advanced
K-Dense-AIK-Dense-AI
33.0k

alphafold-database

Retrieve AlphaFold-predicted protein structures and confidence metrics by UniProt IDs.

Official
Intermediate
SologaSologa
1

torchdrug

Create and apply PyTorch-native Graph Neural Networks for molecular and protein data analysis.

Community
Advanced
sanand0sanand0
8

torchdrug

Predict molecular properties with graph neural networks using PyTorch.

Community
Advanced