bio-virtual-screening
Performs structure-based virtual screening using AutoDock Vina 1.2 for molecular docking. Prepares receptor PDBQT files, generates ligand conformers, defines binding site boxes, and ranks compounds by predicted binding affinity. Use when screening chemical libraries against a protein structure to find potential binders.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-virtual-screening --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.
## Version Compatibility Reference examples tested with: AutoDock Vina 1.2+, RDKit 2024.03+, pandas 2.2+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Virtual Screening **"Dock my compound library against a protein target"** → Perform structure-based virtual screening by preparing a receptor PDBQT, generating ligand conformers, defining a binding site box, and scoring each compound by predicted binding affinity using AutoDock Vina. - Python: `vina.Vina()` for docking, `AllChem.EmbedMolecule()` (RDKit) for conformer generation Screen compound libraries against protein targets using molecular docking. ## Receptor Preparation **Goal:** Prepare a protein structure for molecular docking. **Approach:** Remove waters and heteroatoms from the PDB, add hydrogens at physiological pH, assign Gasteiger charges, and convert to PDBQT format using Open Babel. ```python from rdkit import Chem from rdkit.Chem import AllChem imp
- Version Compatibility
- Receptor Preparation
- Ligand Preparation
- Docking with Vina
- Virtual Screening Pipeline
- Binding Site Definition
- Related Skills
What does the bio-virtual-screening skill do?
Performs structure-based virtual screening using AutoDock Vina 1.2 for molecular docking. Prepares receptor PDBQT files, generates ligand conformers, defines binding site boxes, and ranks compounds by predicted binding affinity. Use when screening chemical libraries against a protein structure to find potential binders.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-virtual-screening --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 FreedomIntelligence/OpenClaw-Medical-Skills, a repository with 2,909 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.