Data Exploration Services

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:

1. Structure and chemical attribute search
2. Sequence search
3. Sequence motif search
4. Structure similarity search
5. Structure motif search
6. Chemical similarity search
7. 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).

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.

As of June 28, 2024, NGL will be removed as a molecular viewer option from RCSB.org Structure Summary Pages (Structure tab). We recommend users to fully transition to using Mol* for 3D visualization. Mol* offers enhanced features and improved performance for visualization needs.

A comprehensive migration guide can help facilitate a smooth transition from NGL to Mol*.

Extensive Mol* documentation is available and is searchable from the top RCSB.org search box. This search tool is available to quickly find answers to questions related to this migration process and for Mol* feature exploration.

Contact info@rcsb.org with any issues or questions about this migration.

As of July 2, 2024, RCSB PDB will no longer serve PDB data in the MMTF compression format. Users are strongly encouraged to switch to accessing the data files offered in the compressed BinaryCIF (BCIF) format.

The MMTF compression format for PDB coordinate data was introduced in 2016 for storing macromolecular 3D coordinate data. Since 2020, the BinaryCIF format has been used by RCSB PDB as the preferred compression data format.

BinaryCIF (BCIF, GitHub) stores text-based CIF files using a more efficient binary encoding. It enables both lossless and lossy compression of the original CIF file.

A new paper introduces a suite of RCSB.org tools tailor-made for efficient management, search, organization, and visualization of experimental PDB structures and Computed Structure Models (CSMs).

RCSB Protein Data Bank: visualizing groups of experimentally determined PDB structures alongside computed structure models of proteins
Joan Segura, Yana Rose, Chunxiao Bi, Stephen K. Burley, Sebastian Bittrich
(2023) Front. Bioinform. 3:1311287 doi:10.3389/fbinf.2023.1311287

Sequence Alignments in 3D tool for the D-galactose/methyl-galactoside binding periplasmic protein (GGBP) related Group at 100% of sequence identity. (Figure 14 of Front. Bioinform. 3:1311287 doi: 10.3389/fbinf.2023.1311287)