| name | pdb-database |
| description | > Use when you want to search for or download experimentally-determined 3D structures for biomolecules (proteins, nucleic acids, bound ligands). Supports searching by sequence similarity, structure similarity, chemical and other attributes. Also use to get metadata about biomolecular structure experiments. |
RCSB Protein Data Bank skill
Prerequisites
uv: Read the uv skill and follow its Setup instructions to ensure
uv is installed and on PATH.- User Notification: If LICENSE_NOTIFICATION.txt does not already exist in
this skill directory then (1) prominently notify the user to check the terms
at https://www.rcsb.org/pages/usage-policy, then (2) create the file
recording the notification text and timestamp.
Core Rules
- Always prefer to use the provided scripts. Only as a last resort use
curl, urllib, raw HTTP requests, or any other method to access PDB APIs.
The scripts automatically enforce required rate limits.
- Always redirect output to a file. Parse output with e.g.
jq, grep,
or a short Python snippet. Do NOT print large API responses to stdout to
avoid truncation.
- Notification: If this skill is used, ensure this is mentioned in the
output.
- Explain your queries On completing a task that used PDB JSON/GraphQL
queries, explain in clear language what your query did so the user can
correct any bad assumptions.
Attribute-based search workflow
-
Fetch the relevant schema to discover searchable attribute names. For
structure attributes: uv run scripts/fetch_schema.py --api search_structure --output schema_structure.txt For chemical attributes: uv run scripts/fetch_schema.py --api search_chemical --output schema_chemical.txt
-
Grep the schema to find relevant attributes. Grep one keyword at a time
and examine many lines — there are lots of similar attributes and you must
choose the best match for the user's intent.
-
Compose and run a JSON search query using the discovered attributes: uv run scripts/search_pdb.py --query '<JSON>' --return_type <RETURN_TYPE> --output results.json Pass the --count_only flag to get just the number
of matching entries.
For step 2: some basic PDB concepts (helpful for attribute choice)
- Entity: A unique molecule found in a structure.
- Instance / Chain: A particular copy of an entity. E.g. if a structure
contains two protein chains with the same sequence, they are the same entity
but different instances / chains.
- Assembly: A biologically relevant collection of instances / chains. This
may be the same as the deposited structure, a subset, or multiple copies.
- Label vs Auth: Polymer instances get letter labels ("A", "B", "AA") and
their monomers are numbered. There are author-assigned ("auth") and
PDB-internal ("label") schemes. The label scheme is more consistent and is
always used in scripts and APIs. However, users and papers may refer to the
author scheme (clarify which scheme is being used if necessary).
- Chemical component: A small molecule / monomer, with an ID matching
[A-Z]{1,3}
- Primary citation: The main publication about a structure. Prefer
primary_citation attributes over citation attributes.
- Resolution: Frequently used measure of structure quality (lower is
better). Usually prefer
rcsb_entry_info.resolution_combined, which
accounts for different experimental methods.
For step 3: Example queries
uv run scripts/search_pdb.py --query '{ "type": "group", "logical_operator": "and", "nodes": [ { "type": "terminal", "service": "text", "parameters": { "operator": "exact_match", "negation": true, "value": "Homo sapiens", "attribute": "rcsb_entity_source_organism.taxonomy_lineage.name" } }, { "type": "terminal", "service": "text", "parameters": { "operator": "exact_match", "value": "Nature", "attribute": "rcsb_primary_citation.rcsb_journal_abbrev" } } ] }' --return_type entry --sort_by rcsb_accession_info.initial_release_date --sort_direction desc --page_start 0 --rows 100 --output results.json
uv run scripts/search_pdb.py --query '{ "type": "terminal", "service": "text_chem", "parameters": { "operator": "exact_match", "value": "CA", "attribute": "rcsb_chem_comp_container_identifiers.comp_id" } }' --return_type entry --output results.json
uv run scripts/search_pdb.py --query '{ "type": "terminal", "service": "text", "parameters": { "operator": "exact_match", "value": "disulfide bridge", "attribute": "rcsb_polymer_struct_conn.connect_type" } }' --return_type entry --count-only --output count.json
Common operators: exact_match, equals, exists, contains_phrase,
contains_words, in, greater, less
Similarity-based search workflow
Similarity searches do not require a schema fetch. Basic examples:
uv run scripts/search_pdb.py --query '{ "query": { "type": "terminal", "service": "sequence", "parameters": { "evalue_cutoff": 1, "identity_cutoff": 0.9, "sequence_type": "protein", "value": "MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQ" } }, "request_options": { "scoring_strategy": "sequence" } }' --return_type polymer_entity --output results.json
uv run scripts/search_pdb.py --query '{ "type": "terminal", "service": "structure", "parameters": { "value": {"entry_id": "6LU7", "asym_id": "A"}, "number_of_candidates": 2000 } }' --return_type polymer_entity --output results.json
uv run scripts/search_pdb.py --query '{ "type": "terminal", "service": "seqmotif", "parameters": { "value": "C-x(2,4)-C-x(3)-[LIVMFYWC]-x(8)-H-x(3,5)-H.", "pattern_type": "prosite", "sequence_type": "protein" } }' --return_type polymer_entity --output results.json
uv run scripts/search_pdb.py --query '{ "type": "terminal", "service": "chemical", "parameters": { "value": "InChI=1S/C8H9NO2/c1-6(10)9-7-2-4-8(11)5-3-7/h2-5,11H,1H3,(H,9,10)", "type": "descriptor", "descriptor_type": "InChI", "match_type": "graph-strict" } }' --return_type mol_definition --output results.json
See https://search.rcsb.org/#search-services for more details.
Full text search workflow
Searches all text associated with an entry. Example:
uv run scripts/search_pdb.py --query '{ "type": "terminal", "service": "full_text", "parameters": { "value": "isopeptide + ( collagen | fibrinogen )" } }' --return_type entry --output results.json
Important: use full_text search as a last resort when there's no
more precise attribute search available. Consider using the struct.title or
rcsb_pubmed_abstract_text attributes instead.
File download workflow
To download full PDB entries, use the download_coordinate_files.py script. Use
this when you need access to atomic coordinates, when asked for a pdb / mmcif
file, or when non-specifically asked to fetch a PDB code. Example:
uv run scripts/download_coordinate_files.py --ids "4HHB,6BEA" --format "mmcif" --output_dir <OUTPUT_DIR>
Metadata query workflow
This flow is significantly more efficient than downloading full coordinate files
when you only need a few pieces of metadata about each entry / entity.
-
Fetch the schema for the relevant object type. E.g. uv run scripts/fetch_schema.py --api data_entry --output schema_entry.txt
-
Grep the schema for relevant fields (one keyword at a time, many lines).
-
Compose and run a GraphQL metadata query: uv run scripts/fetch_pdb_metadata.py --query '<GraphQL>' --output results.json
For step 3: Example queries
uv run scripts/fetch_pdb_metadata.py --query '{ entries(entry_ids: ["1STP", "2JEF", "1CDG"]) { rcsb_id struct { title } exptl { method } } }' --output results.json
uv run scripts/fetch_pdb_metadata.py --query '{ polymer_entities(entity_ids:["2CPK_1","3WHM_1","2D5Z_1"]) { rcsb_id rcsb_entity_source_organism { ncbi_taxonomy_id ncbi_scientific_name } rcsb_cluster_membership { cluster_id identity } } }' --output results.json
uv run scripts/fetch_pdb_metadata.py --query '{ entries(entry_ids:["7NHM", "5L2G"]){ polymer_entities { rcsb_id rcsb_polymer_entity_container_identifiers { reference_sequence_identifiers { database_accession database_name } } } } }' --output results.json
