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DiffDock

Maintainer K-Dense Inc. · Last updated April 1, 2026

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. **Core Capabilities:** - Predict ligand binding poses with high accuracy using deep learning - Support protein structures (PDB files) or sequence….

Claude CodeOpenClawNanoClawAnalysisReproductiondiffdockchemistrypackagecheminformatics & drug discovery

Original source

K-Dense-AI/claude-scientific-skills

https://github.com/K-Dense-AI/claude-scientific-skills/tree/main/scientific-skills/diffdock

Maintainer: K-Dense Inc.
License: MIT license
Last updated: April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

Predict ligand binding poses with high accuracy using deep learning.
Support protein structures (PDB files) or sequences (via ESMFold).
Process single complexes or batch virtual screening campaigns.
Generate confidence scores to assess prediction reliability.
Handle diverse ligand inputs (SMILES, SDF, MOL2).

Source Doc

Excerpt From SKILL.md

When to Use This Skill

This skill should be used when:

"Dock this ligand to a protein" or "predict binding pose"
"Run molecular docking" or "perform protein-ligand docking"
"Virtual screening" or "screen compound library"
"Where does this molecule bind?" or "predict binding site"
Structure-based drug design or lead optimization tasks
Tasks involving PDB files + SMILES strings or ligand structures
Batch docking of multiple protein-ligand pairs

Check Environment Status

Before proceeding with DiffDock tasks, verify the environment setup:


## Installation Options

**Option 1: Conda (Recommended)**

**Option 2: Docker**

**Important Notes:**
- GPU strongly recommended (10-100x speedup vs CPU)
- First run pre-computes SO(2)/SO(3) lookup tables (~2-5 minutes)
- Model checkpoints (~500MB) download automatically if not present

Use cases

Dock this ligand to a protein" or "predict binding pose.
Run molecular docking" or "perform protein-ligand docking.
Virtual screening" or "screen compound library.
Where does this molecule bind?" or "predict binding site.

Not for

Do not rely on this catalog entry alone for installation or maintenance details.

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