Related Experiment Video
Updated: Jul 8, 2025
09:51
Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
Published on: July 16, 2017
15.5K
RCSB Protein Data Bank: visualizing groups of experimentally determined PDB structures alongside computed structure
Joan Segura1, Yana Rose1, Chunxiao Bi1
1Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, San Diego, CA, United States.
Frontiers in Bioinformatics
|December 19, 2023
Summary
Artificial intelligence tools now predict protein 3D structures, creating vast new data. The RCSB PDB portal offers new tools to manage, search, and visualize this growing collection of protein structures.
Area of Science:
- Structural biology
- Bioinformatics
- Computational biology
Background:
- Artificial intelligence (AI) and machine learning (ML) models like AlphaFold, RosettaFold, and ESMFold accurately predict protein 3D structures from amino acid sequences.
- These AI tools generate unprecedented volumes of structural data from proteomes and metagenomic studies.
- Existing data management and visualization tools struggle to handle this exponential increase in biomolecular structure information.
Purpose of the Study:
- To introduce a suite of tools for managing, searching, organizing, and visualizing large collections of 3D protein structures.
- To address the need for efficient handling of both experimental and computationally predicted protein structure data.
- To provide researchers with advanced visualization capabilities for exploring multiple sequence and structural alignments.
Main Methods:
- Development and deployment of a new suite of tools on the RCSB PDB research-focused web portal (RCSB.org).
- Integration of capabilities for managing, searching, clustering, and visualizing large sets of 3D macromolecular structures.
- Implementation of features for summarizing and visualizing metadata, biological/biochemical annotations, and structural features.
- Inclusion of advanced visualization techniques for interactive exploration of sequence and structure alignments.
Main Results:
- A comprehensive suite of tools is now available on RCSB.org for researchers.
- The tools facilitate efficient management and exploration of both experimental and predicted protein structure data.
- Enhanced visualization capabilities allow for interactive analysis of multiple sequence and structural alignments.
- The platform supports the burgeoning corpus of 3D macromolecular structure data.
Conclusions:
- The new RCSB PDB tools are essential for researchers dealing with large-scale protein structure data.
- These tools enable efficient data handling, search, and visualization, accelerating scientific discovery.
- The platform supports the integration and analysis of diverse structural data, including AI-predicted models.
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