Use a Python Package to Access the RCSB PDB Search API

02/12

RCSB PDB now maintains a Python package (rcsbsearchapi) that can be used for accessing our Search API.

The package can be installed from PyPI or by downloading the source code on GitHub. This repository will serve as the central hub for all future development, bug fixes, and discussions related to the RCSB PDB Search API package.

With this package, users can perform all the same types of queries they are familiar with from the Advanced Search builder on RCSB.org, all through a Pythonic interface. These capabilities include:

Structure and chemical attribute search
Sequence search
Sequence motif search
Structure similarity search
Structure motif search
Chemical similarity search
Option to include computed structure models (CSMs) in search

A full overview with examples is available. Users are encouraged to review the examples in the README file, Quickstart tutorial, and Jupyter notebook.

This Python wrapper was developed by undergraduates Rusham Bhatt (University of Maryland Baltimore County) and Santiago Blaumann (Cornell University) under the direction of Dennis Piehl and Brinda Vallat (RCSB PDB) as part of the Rutgers RISE (Research Intensive Summer Experience).

Brinda Vallat, Santiago Blaumann, Rusham Bhatt, Dennis Piehl. Applications for the 2024 Research Intensive Experience at Rutgers are open now.

RCSB PDB appreciates all RCSB PDB API contributors, with special thanks Spencer Bliven (@sbliven) for providing the original groundwork for the package, and Rutgers undergraduate Pratyoy Biswas for expanding the work performed during the RISE at Rutgers program.

The Data API and Search API are the two main APIs that power RCSB.org. The Data API serves to retrieve data based on PDB ID while the Search API retrieves PDB IDs that match given conditions. Detailed documentation on RCSB PDB Web Service APIs is available.

Stay up-to-date with API developments by viewing (or subscribing) to the RCSB PDB API announcements Google group.