drug-db-pdb
OfficialRetrieve drug-target PDB structures with ligands
Education & Research#drug discovery#metadata extraction#api search#protein structures#rcsb pdb#ligand retrieval#mmcif downloads
Authorlearningmatter-mit
Version1.0.0
Installs0
System Documentation
What problem does it solve?
This Skill automates finding protein (and protein–ligand complex) structures in the RCSB Protein Data Bank and packaging the metadata and optional downloads needed for drug-discovery modeling.
Core Features & Use Cases
- RCSB Search + Ranking: Uses the RCSB Search API to return top-scoring PDB IDs for a query (optionally filtered by organism, resolution, and experimental method).
- Rich Entry Metadata Retrieval: Fetches entry core metadata including title, experimental method, resolution, release dates, and unit cell parameters.
- Ligand/Non-polymer Entity Extraction: Enumerates non-polymer entities from the entry container identifiers and retrieves bound ligand metadata.
- Optional File Downloads: Downloads coordinate files in PDB or preferred mmCIF formats and can also download wwPDB full validation report PDFs.
- Quality-Aware Workflow Support: Encourages selection using validation/ligand-quality rather than resolution alone.
Quick Start
Use the drug-db-pdb skill to search RCSB PDB for ACE2 Homo sapiens X-ray diffraction structures with resolution <= 2.5 Å and write the resulting metadata to a JSON file.
Dependency Matrix
Required Modules
None requiredComponents
scripts
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Please help me install this Skill: Name: drug-db-pdb Download link: https://github.com/learningmatter-mit/AtomisticSkills/archive/main.zip#drug-db-pdb Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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