drug-protein-prep
OfficialClean and protonate receptors for docking
Education & Research#molecular docking#docking#rcsb#pdbfixer#protein preparation#pdbqt#hydrogenation
Authorlearningmatter-mit
Version1.0.0
Installs0
System Documentation
What problem does it solve?
This Skill fixes common macromolecular receptor preparation issues (missing atoms/residues, nonstandard residues, and absent hydrogens) so structures are suitable for docking or simulation.
Core Features & Use Cases
- RCSB-based or local input preparation: Fetch PDB/mmCIF by PDB ID (optionally a biological assembly) or start from a local receptor file.
- Structure cleanup and protonation: Uses PDBFixer/OpenMM to handle missing residues/atoms, replace nonstandard residues, and add hydrogens at a target pH for docking readiness.
- Docking-format conversion: Converts the prepared receptor PDB to PDBQT via the
mcp_drugdisc_convert_to_pdbqttool (Meeko) for AutoDock Vina.
Quick Start
Ask the agent to prepare receptor 1IEP chain A for docking at pH 7.0 and output the cleaned PDB plus a PDBQT conversion.
Dependency Matrix
Required Modules
pdbfixeropenmm
Components
scriptsreferences
💻 Claude Code Installation
Recommended: Let Claude install automatically. Simply copy and paste the text below to Claude Code.
Please help me install this Skill: Name: drug-protein-prep Download link: https://github.com/learningmatter-mit/AtomisticSkills/archive/main.zip#drug-protein-prep Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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