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DiffDock Molecular Docking Skill

Runs DiffDock/DiffDock-L to predict protein–small-molecule binding poses and interprets the confidence scores.

Data & AnalyticsAdvanced★ 33,030⑂ 3,248AI score 8/10Last updated: Aug 9, 2026

What it does

  • Builds correct DiffDock inference commands from a PDB file or protein sequence plus SMILES/SDF/MOL2 ligand input.
  • Covers single-complex docking, CSV-driven batch docking, and virtual screening with pre-computed ESM embeddings.
  • Explains the rank/confidence output files and the confidence bands (>0 high, -1.5 to 0 moderate, <-1.5 low).
  • Guides parameter tuning (samples_per_complex, inference_steps, torsion temperature), ensemble docking, and rescoring with GNINA or MM/GBSA.

Who it's for

  • Computational chemists and bioinformaticians doing structure-based drug design or lead optimization.
  • Users comfortable with conda/Docker and ideally a CUDA GPU.
  • Screening teams that need to generate, filter, and rank many poses.

Examples

  1. "Dock aspirin into this PDB" → run python -m inference --protein_path protein.pdb --ligand_description "CC(=O)Oc1ccccc1C(=O)O" and interpret rank1.
  2. Screen a 200-compound library: validate the batch CSV, pre-compute embeddings, run batch inference, then analyze_results.py --export summary.csv.
  3. Ensemble-dock one ligand against three protein conformers to look for consensus poses.

Note: it does not predict binding affinity (ΔG, Kd) and is unsuitable for protein–protein docking, covalent docking, or long peptides.

· · · Install guide · · ·

Try it now, no install

Paste this into Claude to use the skill without installing anything.

Read the instructions in this file and follow them to help me:
https://raw.githubusercontent.com/K-Dense-AI/scientific-agent-skills/HEAD/skills/diffdock/SKILL.md

What I want: (describe your task here)

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↓ If it works for you, download the ZIP below and install it. Then it runs on its own — no pasting each time.

Install in the Claude app (no terminal)
  1. Download the ZIP with the button below.
  2. In Claude, open Settings → Capabilities and turn on 'Code execution and file creation'. (one time)
  3. Go to Customize → Skills → + → 'Upload a skill' and upload the ZIP.
↓ Download ZIP
Install in Claude Code

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Install the skill I found on AI Skill Mart.
Copy the skills/diffdock folder from the GitHub repo K-Dense-AI/scientific-agent-skills into my ~/.claude/skills/diffdock/.
When it's done, tell me in one line what this skill can do.

Install with a command instead

git clone https://github.com/K-Dense-AI/scientific-agent-skills.git && mkdir -p ~/.claude/skills && cp -r scientific-agent-skills/skills/diffdock ~/.claude/skills/

⚠ This is a third-party skill. Check the source repository before installing.

  1. Open a terminal.
  2. Clone the skill repo: git clone https://github.com/K-Dense-AI/scientific-agent-skills.git
  3. Copy the skill in: mkdir -p ~/.claude/skills && cp -r scientific-agent-skills/skills/diffdock ~/.claude/skills/
  4. Install DiffDock itself: git clone https://github.com/gcorso/DiffDock.git && cd DiffDock && conda env create --file environment.yml && conda activate diffdock (or docker pull rbgcsail/diffdock).
  5. Verify dependencies with python scripts/setup_check.py (Python, PyTorch/CUDA, PyG, RDKit).
  6. Restart Claude Code and ask something like "dock this ligand to this protein" to trigger the skill.
View source on GitHub ↗License: MIT