autodock-vina-docking
Molecular docking with AutoDock Vina (Python API). Receptor/ligand prep (Meeko + RDKit), grid box, docking, pose and binding energy analysis, and batch virtual screening.
npx skills add BioTender-max/awesome-bio-agent-skills --skill autodock-vina-docking --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# AutoDock Vina Molecular Docking ## Overview AutoDock Vina is one of the fastest and most widely used open-source molecular docking engines for predicting protein–ligand binding modes and affinities. This skill covers the full Python-based pipeline: receptor preparation from PDB, ligand preparation from SMILES/SDF via Meeko and RDKit, search box definition, docking execution, pose analysis, and batch virtual screening for hit identification. ## When to Use - Predicting binding poses of small molecules to a protein target - Estimating relative binding affinities (kcal/mol) for ligand ranking - Virtual screening of compound libraries against a target receptor - Validating docking protocols by re-docking co-crystallized ligands - Preparing docking inputs from SMILES strings without intermediate files - Comparing binding modes of analogs in a structure-activity relationship study - Generating starting poses for molecular dynamics simulations - Use **DiffDock** instead for blind docking when the binding site is unknown; use **GNINA** as an alternative with CNN scoring ## Prerequisites - **Python packages**: `vina`, `meeko`, `rdkit`, `prody` (for PDB fetch), `py3Dmol` (for visualization
- Overview
- When to Use
- Prerequisites
- Workflow
- Step 1: Fetch and Prepare the Receptor
- Step 2: Identify the Binding Site
- Step 3: Prepare the Ligand from SMILES
- Step 4: Run Docking
- Step 5: Analyze Docking Results
- Step 6: Visualize Docking Results
- Step 7: Batch Virtual Screening
- Step 8: Save and Export
- Key Parameters
- Common Recipes
pip install vina meeko rdkit-pypi prody py3Dmol ADFR Suite must be installed separately for prepare_receptor
What does the autodock-vina-docking skill do?
Molecular docking with AutoDock Vina (Python API). Receptor/ligand prep (Meeko + RDKit), grid box, docking, pose and binding energy analysis, and batch virtual screening.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill autodock-vina-docking --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.