Overview
diffdock is an open-source data skill for Claude Code and compatible agents, published by K-Dense-AI. Its author describes it as: “DiffDock and DiffDock-L molecular docking. Use for protein-small-molecule pose prediction from PDB or sequence plus SMILES/SDF/MOL2, batch docking, virtual screening, and pose-confidence interpretation. Not for bindin…”. The project has 34k stars on GitHub and is available under the MIT license. Add it to your setup with `git clone https://github.com/K-Dense-AI/scientific-agent-skills ~/.claude/skills/diffdock`.
What diffdock does
DiffDock is a diffusion-based deep learning tool for molecular docking that predicts 3D binding poses of small molecule ligands to protein targets. It represents the state-of-the-art in computational docking, crucial for structure-based drug discovery and chemical biology.
What’s inside
The SKILL.md for diffdock is organised into these sections:
- Overview
- When to Use This Skill
- Installation and Environment Setup
- Check Environment Status
- Installation Options
- Core Workflows
- Workflow 1: Single Protein-Ligand Docking
- Workflow 2: Batch Processing Multiple Complexes
- Workflow 3: Analyzing Results
- Confidence Score Interpretation
- Parameter Customization
- Using Custom Configuration
Installation
Add diffdock to your agent with:
git clone https://github.com/K-Dense-AI/scientific-agent-skills ~/.claude/skills/diffdockReview a skill’s source before installing it — skills can instruct your agent to run commands. This command comes from the skill’s public repository, which is the source of truth for setup steps. New to skills? Read how to install Claude Code skills.
Supported agents
Neither the skill nor its repository names a specific agent. It uses the SKILL.md format, which several agents can load — check the repository for any agent-specific requirements.
License
diffdock is published under the MIT license.
Strengths
- Clear MIT license — safe to read and adapt within its terms
- Ships in K-Dense-AI/scientific-agent-skills, an established project with 33,821 GitHub stars
- Actively maintained — repository updated in the last 90 days
Author
Topics
Frequently asked questions
- What does diffdock do?
- DiffDock and DiffDock-L molecular docking. Use for protein-small-molecule pose prediction from PDB or sequence plus SMILES/SDF/MOL2, batch docking, virtual screening, and pose-confidence interpretation. Not for binding affinity prediction.
- How do I install diffdock?
- Run git clone https://github.com/K-Dense-AI/scientific-agent-skills ~/.claude/skills/diffdock in your agent, then reload your skills. Review the source at https://github.com/K-Dense-AI/scientific-agent-skills before installing.
- Is diffdock free to use?
- Yes. diffdock is free and open source under the MIT license, so you can read, run, and adapt it within that license's terms.
- Where does diffdock come from?
- diffdock ships inside K-Dense-AI/scientific-agent-skills, a repository that contains 42 catalogued skills in total. The repository's 33,821 GitHub stars apply to that whole collection, not to this skill on its own.