diffdock
Category: chemistry-and-drug-discovery · License: MIT · Version: 1.3 · Includes scripts
Tags: molecular docking, virtual screening, structural biology, drug discovery
When to use it
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.Example requests
Ask your agent in plain language, for example:- “Dock this SMILES CC(=O)Oc1ccccc1C(=O)O into my protein.pdb and give me the top poses.”
- “I have 240 compounds in screen_hits.csv (columns: name, smiles) and a kinase structure 5ZZZ_clean.pdb. I ran inference.py and got CUDA out of memory partway through the batch. How do I set this up as a batch run and get it to finish, and then rank the results?”
- “I only have the amino acid sequence of my target, no crystal structure, and a small molecule I drew in an SDF. I want to know where on the protein it likely sits and how sure the model is about that, since I don’t know the binding site.”
Install
/plugin marketplace add KalarisLabs/research-agent-skills and install the whole chemistry-and-drug-discovery category with /plugin install chemistry-and-drug-discovery@research-agent-skills.