News 2024
Celebrate DNA Day on April 25
04/21
April 22 is Earth Day
04/18
Spring Newsletter Published
04/16
Paper Published: Folding paper models of biostructures for outreach and education
04/14
Register Now for a Webinar on Understanding PDB Validation: Which experimental structures should I rely on?
04/09
Video: Immunology and Cancer
04/02
Register Now for a Virtual Deep Dive into Computed Structure Model Exploration at RCSB.org
04/01
Explore Mechanism and Catalytic Site Annotations
03/31
Take the EDMAPS.rcsb.org Survey
03/29
Education Corner: Bringing Proteins to Life
03/26
Register for the April 1 Mol* Virtual Office Hour
03/24
March 24 is World TB Day
03/21
Meet RCSB PDB at the #DiscoverBMB Meeting
03/20
Paper Published: Visualizing groups of PDB structures and CSMs
03/17
March 11-17: Brain Awareness Week
03/11
Poster Prize Awarded at The Biophysical Society Meeting
03/06
March 4 is International HPV Awareness Day
02/29
February 29 is Rare Disease Day
02/27
Register for the March 28 Office Hour to Ask A Biocurator
02/25
PDB-101 Focus: Peak Performance
02/16
Use a Python Package to Access the RCSB PDB Search API
02/12
Molecular Valentines
02/11
Meet RCSB PDB at The Biophysical Society Meeting
02/06
February 4 is World Cancer Day
02/01
Register for VIZBI 2024 (March 13–15)
01/30
Notice: NGL Viewer Deprecation
01/30
Prizes Awarded at The Biophysical Society Japan Meeting
01/28
Take the CSM User Survey and Win
01/24
Register for the February 13 Mol* Webinar
01/19
Undergrads: Spend your summer with RCSB PDB
01/18
Register for the February 5 RCSB.org Office Hour
01/16
Celebrate #NationalMilkDay
01/10
Winter Newsletter Published
01/08
Applications Open for Director
01/07
Top Molecules of the Month in 2023
01/04

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).

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

<I>Detailed documentation on RCSB PDB Web Service APIs is available.</I>Detailed documentation on RCSB PDB Web Service APIs is available.


Past news and events have been reported at the RCSB PDB website and past Newsletters.