pdb-database

Files (4)

• SKILL.md
• api_reference.md · references/
• query.cpython-313.pyc · scripts/__pycache__/
• query.py · scripts/

SKILL.md (first lines)

# 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.

## Query Limitations — Read Before Using

PDB stores **experimentally determined 3D structures of proteins and nucleic acids**. Queries must target a protein, gene, or known PDB ID. Drug/chemistry phrases return zero results.

| ❌ Fails (not a structure query) | ✅ Works |
|---|---|
| "KRAS covalent inhibitors" | "KRAS" → returns KRAS structures |
| "covalent warhead selectivity" | "6OIM" (direct PDB ID for KRAS-G12C/AMG-510) |
| "BTK warhead optimization" | "BTK" or "Q06187" |
| "kinase inhibitor selectivity" | "EGFR kinase" |

**Rule:** Pass only the protein/gene name or PDB ID. Never pass a drug concept or mechanism phrase. If you have a UniProt accession, use the cross-references in that entry to get specific PDB IDs, then pass those here.

## 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"])
```

From lamm-mit/scienceclaw, Apache-2.0.

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