rcsb-api - Access RCSB PDB APIs and data from Python¶
The rcsb-api package provides a Python interface to
RCSB PDB API services.
Use it to search and fetch macromolecular structure data from RCSB PDB at RCSB.org.
Availability¶
Install it from PyPI via pip or uv:
pip install rcsb-api
# or, if using uv:
uv pip install rcsb-api
Or, download from GitHub
Overview¶
The rcsb-api package provides a simple Pythonic interface to the suite of RCSB PDB APIs for querying and fetching data in the PDB. Specifically, each API service is provided as a separate “module” (or sub-package) within the Python client, and offers the following set of key functionalities:
Search API module (
rcsbapi.search):Perform all search types available through the RCSB.org Advanced Search builder (e.g., full-text, attribute-based, sequence and structure similarity, sequence and structure motif)
Use simple Boolean logic to intuitively construct complex or nested queries
Upload custom structure files for structure similarity searches
Include computed structure models (CSMs) in search results
Data API module (
rcsbapi.data):Retrieve any subset of metadata, features, and/or annotations for a given list of PDB IDs (e.g., experimental method details, structural annotations, binding sites, etc.)
Easily fetch data for all structures across the archive
Simplified GraphQL query construction using a Python syntax
Sequence Coordinate API module (
rcsbapi.sequence):Query alignments between structural and sequence databases as well as protein positional annotations/features integrated from multiple resources
Alignment data is available for NCBI RefSeq (including protein and genomic sequences), UniProt and PDB sequences
Protein positional features are integrated from UniProt, CATH, SCOPe and RCSB PDB and collected from the RCSB PDB Data Warehouse
Model API module (
rcsbapi.model):Provides access to molecular structure data (e.g., atomic coordinates) and related information (in mmCIF or BCIF formats)
Query for various structural data types, such as full structure, ligands, atoms, residue interactions, and more
Valuable for extracting out specific slices of a structure data file (not for bulk downloads, in which case see our download services)
Training Materials¶
Example usage for each module is available throughout these documentation pages (see sidebar menu navigation)
The project source code is available on GitHub, which also contains several example Jupyter notebooks for all supported API services.
Watch our webinar, Streamlining Access to RCSB PDB APIs with Python, which provides an introduction to our Search and Data APIs along with hands-on tutorials.
Contents¶
Search API
Data API
Sequence Coordinates API
Model Server API
Citing¶
Please cite the rcsb-api package with the following reference:
Dennis W. Piehl, Brinda Vallat, Ivana Truong, Habiba Morsy, Rusham Bhatt, Santiago Blaumann, Pratyoy Biswas, Yana Rose, Sebastian Bittrich, Jose M. Duarte, Joan Segura, Chunxiao Bi, Douglas Myers-Turnbull, Brian P. Hudson, Christine Zardecki, Stephen K. Burley. rcsb-api: Python Toolkit for Streamlining Access to RCSB Protein Data Bank APIs, Journal of Molecular Biology, 2025. DOI: https://doi.org/10.1016/j.jmb.2025.168970
You should also cite the RCSB.org API services this package utilizes:
Yana Rose, Jose M. Duarte, Robert Lowe, Joan Segura, Chunxiao Bi, Charmi Bhikadiya, Li Chen, Alexander S. Rose, Sebastian Bittrich, Stephen K. Burley, John D. Westbrook. RCSB Protein Data Bank: Architectural Advances Towards Integrated Searching and Efficient Access to Macromolecular Structure Data from the PDB Archive, Journal of Molecular Biology, 2020. DOI: https://doi.org/10.1016/j.jmb.2020.11.003