Agent skill · research science · aiskillstore
pdb-database
Access RCSB PDB for 3D protein/nucleic acid structures. Search by text/sequence/structure, download coordinates (PDB/mmCIF), retrieve metadata, for structural biology and drug discovery.
Why this skill is useful
Provides specific commands and queries for accessing and manipulating PDB data that the AI wouldn't reliably generate on its own.
What it needs
Requires rcsb account access. About 4k tokens when loaded. Last updated 2026-08-07. 405 stars on the source repository.
What this skill does
PDB Database Overview RCSB PDB is the worldwide repository for 3D structural data of biological macromolecules. Search for structures, retrieve coordinates and metadata, perform sequence and structure similarity searches across 200,000+ experimentally determined structures and computed models. When to Use This Skill This skill should be used when: Searching for protein or nucleic acid 3D structures by text, sequence, or structural similarity Downloading coordinate files in PDB, mmCIF, or BinaryCIF formats Retrieving structural metadata, experimental methods, or quality metrics Performing batch operations across multiple structures Integrating PDB data into computational workflows for drug discovery, protein engineering, or structural biology research Core Capabilities 1. Searching for Structures Find PDB entries using various search criteria: Text Search: Search by protein name, keywords, or descriptions Attribute Search: Query specific properties (organism, resolution, method, etc.) Sequence Similarity: Find structures similar to a given sequence Structure Similarity: Find structures with similar 3D geometry Combining Queries: Use logical operators to build complex searches 2. Retrieving Structure Data Access detailed information about specific PDB entries: Basic Entry Information: Polymer Entity Information: Using GraphQL for Flexible Queries: 3. Downloading Structure Files Retrieve coordinate files in various formats: Download Methods: PDB format (legacy text format): https://files.rcsb.org/download/{PDBID}.pdb mmCIF format (modern standard): https://files.rcsb.org/download/{PDBID}.cif BinaryCIF (compressed binary): Use ModelServer API for efficient access Biological assembly: https://files.rcsb.org/download/{PDBID}.pdb1 (for assembly 1) Example Download: 4. Working with Structure Data Common operations with retrieved structures: Parse and Analyze Coordinates: Use BioPython or other structural biology libraries to work with downloaded files: Extract Metadata: 5. …
How to use it
Reference it in AdaL, Claude Code, Cursor or any coding agent — nothing to install:
@skills aiskillstore/pdb-database--42eeab