pdb-database — Доступ и обработка данных RCSB Protein Data Bank

--- name: pdb-database description: 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. license: Unknown metadata: skill-author: K-Dense Inc. --- # 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 ```python from rcsbapi.search import TextQuery query = TextQuery("hemoglobin") results = list(query()) print(f"Found {len(results)} structures") ``` **Attribute Search:** Query specific properties (organism, resolution, method, etc.) ```python from rcsbapi.search import AttributeQuery from rcsbapi.search.attrs import rcsb_entity_source_organism # Find human protein structures query = AttributeQuery( attribute=rcsb_entity_source_organism.scientific_name, operator="exact_match", value="Homo sapiens" ) results = list(query()) ``` **Sequence Similarity:** Find structures similar to a given sequence ```python from rcsbapi.search import SequenceQuery query = SequenceQuery( value="MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKEKMSKDGKKKKKKSKTKCVIM", evalue_cutoff=0.1, identity_cutoff=0.9 ) results = list(query()) ``` **Structure Similarity:** Find structures with similar 3D geometry ```python from rcsbapi.search import StructSimilarityQuery query = StructSimilarityQuery( structure_search_type="entry", entry_id="4HHB" # Hemoglobin ) results = list(query()) ``` **Combining Queries:** Use logical operators to build complex searches ```python from rcsbapi.search import TextQuery, AttributeQuery from rcsbapi.search.attrs import rcsb_entry_info # High-resolution human proteins query1 = AttributeQuery( attribute=rcsb_entity_source_organism.scientific_name, operator="exact_match", value="Homo sapiens" ) query2 = AttributeQuery( attribute=rcsb_entry_info.resolution_combined, operator="less", value=2.0 ) combined_query = query1 & query2 # AND operation results = list(combined_query()) ``` ### 2. Retrieving Structure Data Access detailed information about specific PDB entries: **Basic Entry Information:** ```python from rcsbapi.data import Schema, fetch # Get entry-level data entry_data = fetch("4HHB", schema=Schema.ENTRY) print(entry_data["struct"]["title"]) print(entry_data["exptl"][0]["method"]) ``` **Polymer Entity Information:** ```python # Get protein/nucleic acid information entity_data = fetch("4HHB_1", schema=Schema.POLYMER_ENTITY) print(entity_data["entity_poly"]["pdbx_seq_one_letter_code"]) ``` **Using GraphQL for Flexible Queries:** ```python from rcsbapi.data import fetch # Custom GraphQL query query = """ { entry(entry_id: "4HHB") { struct { title } exptl { method } rcsb_entry_info { resolution_combined deposited_atom_count } } } """ data = fetch(query_type="graphql", query=query) ``` ### 3. Downloading Structure Files Retrieve coordinate files in various formats: **Download Methods:** - **PDB format** (legacy text format): `https://files.rcsb.org/download/{PDB_ID}.pdb` - **mmCIF format** (modern standard): `https://files.rcsb.org/download/{PDB_ID}.cif` - **BinaryCIF** (compressed binary): Use ModelServer API for efficient access - **Biological assembly**: `https://files.rcsb.org/download/{PDB_ID}.pdb1` (for assembly 1) **Example Download:** ```python import requests pdb_id = "4HHB" # Download PDB format pdb_url = f"https://files.rcsb.org/download/{pdb_id}.pdb" response = requests.get(pdb_url) with open(f"{pdb_id}.pdb", "w") as f: f.write(response.text) # Download mmCIF format cif_url = f"https://files.rcsb.org/download/{pdb_id}.cif" response = requests.get(cif_url) with open(f"{pdb_id}.cif", "w") as f: f.write(response.text) ``` ### 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: ```python from Bio.PDB import PDBParser parser = PDBParser() structure = parser.get_structure("protein", "4HHB.pdb") # Iterate through atoms for model in structure: for chain in model: for residue in chain: for atom in residue: print(atom.get_coord()) ``` **Extract Metadata:** ```python from rcsbapi.data import fetch, Schema # Get experimental details data = fetch("4HHB", schema=Schema.ENTRY) resolution = data.get("rcsb_entry_info", {}).get("resolution_combined") method = data.get("exptl", [{}])[0].get("method") deposition_date = data.get("rcsb_accession_info", {}).get("deposit_date") print(f"Resolution: {resolution} Å") print(f"Method: {method}") print(f"Deposited: {deposition_date}") ``` ### 5. Batch Operations Process multiple structures efficiently: ```python from rcsbapi.data import fetch, Schema pdb_ids = ["4HHB", "1MBN", "1GZX"] # Hemoglobin, myoglobin, etc. results = {} for pdb_id in pdb_ids: try: data = fetch(pdb_id, schema=Schema.ENTRY) results[pdb_id] = { "title": data["struct"]["title"], "resolution": data.get("rcsb_entry_info", {}).get("resolution_combined"), "organism": data.get("rcsb_entity_source_organism", [{}])[0].get("scientific_name") } except Exception as e: print(f"Error fetching {pdb_id}: {e}") # Display results for pdb_id, info in results.items(): print(f"n{pdb_id}: {info['title']}") print(f" Resolution: {info['resolution']} Å") print(f" Organism: {info['organism']}") ``` ## Python Package Installation Install the official RCSB PDB Python API client: ```bash # Current recommended package uv pip install rcsb-api # For legacy code (deprecated, use rcsb-api instead) uv pip install rcsbsearchapi ``` The `rcsb-api` package provides unified access to both Search and Data APIs through the `rcsbapi.search` and `rcsbapi.data` modules. ## Common Use Cases ### Drug Discovery - Search for structures of drug targets - Analyze ligand binding sites - Compare protein-ligand complexes - Identify similar binding pockets ### Protein Engineering - Find homologous structures for modeling - Analyze sequence-structure relationships - Compare mutant structures - Study protein stability and dynamics ### Structural Biology Research - Download structures for computational analysis - Build structure-based alignments - Analyze structural features (secondary structure, domains) - Compare experimental methods and quality metrics ### Education and Visualization - Retrieve structures for teaching - Generate molecular visualizations - Explore structure-function relationships - Study evolutionary conservation ## Key Concepts **PDB ID:** Unique 4-character identifier (e.g., "4HHB") for each structure entry. AlphaFold and ModelArchive entries start with "AF_" or "MA_" prefixes. **mmCIF/PDBx:** Modern file format that uses key-value structure, replacing legacy PDB format for large structures. **Biological Assembly:** The functional form of a macromolecule, which may contain multiple copies of chains from the asymmetric unit. **Resolution:** Measure of detail in crystallographic structures (lower values = higher detail). Typical range: 1.5-3.5 Å for high-quality structures. **Entity:** A unique molecular component in a structure (protein chain, DNA, ligand, etc.). ## Resources This skill includes reference documentation in the `references/` directory: ### references/api_reference.md Comprehensive API documentation covering: - Detailed API endpoint specifications - Advanced query patterns and examples - Data schema reference - Rate limiting and best practices - Troubleshooting common issues Use this reference when you need in-depth information about API capabilities, complex query construction, or detailed data schema information. ## Additional Resources - **RCSB PDB Website:** https://www.rcsb.org - **PDB-101 Educational Portal:** https://pdb101.rcsb.org - **API Documentation:** https://www.rcsb.org/docs/programmatic-access/web-apis-overview - **Python Package Docs:** https://rcsbapi.readthedocs.io/ - **Data API Documentation:** https://data.rcsb.org/ - **GitHub Repository:** https://github.com/rcsb/py-rcsb-api