Protein Structure Database (AlphaFold & PDB)

Access the AlphaFold Protein Structure Database and Protein Data Bank (PDB) for structural biology research, drug target analysis, and molecular interaction studies. This skill enables querying protein structures by gene name, UniProt accession, or PDB ID, retrieving 3D structural data, analyzing binding sites and protein-ligand interactions, and comparing predicted (AlphaFold) and experimentally determined (PDB) structures.

Quick Install

npx skills add Open-Medica/open-medical-skills --skill protein-structure-analysis

What It Does

• Structure retrieval: Queries AlphaFold DB and PDB by UniProt accession number, gene symbol, protein name, or PDB ID to retrieve atomic coordinates, confidence scores (pLDDT for AlphaFold), resolution data (for experimental structures), and associated metadata
• Binding site analysis: Identifies known ligand binding sites, catalytic residues, and allosteric pockets from PDB co-crystal structures, mapping residue-level interactions (hydrogen bonds, hydrophobic contacts, pi-stacking, salt bridges) between proteins and bound molecules
• Structure comparison: Aligns predicted AlphaFold models against experimentally determined PDB structures to assess prediction accuracy, identify regions of high uncertainty (low pLDDT / high PAE), and evaluate whether the predicted structure is suitable for downstream computational studies
• Variant impact mapping: Maps clinically relevant amino acid variants onto 3D structures to assess whether mutations occur in functionally important regions (active sites, protein-protein interfaces, transmembrane domains, signal peptides) that could explain pathogenicity
• Drug target assessment: Evaluates protein structures for druggability by analyzing surface pocket geometry, hydrophobicity, and comparison with known drug target families, supporting early-stage drug discovery and repurposing efforts

Clinical Use Cases