RCSB protein Data Bank: exploring protein 3D similarities via comprehensive structural alignments

Area of Science:

• Structural Biology
• Bioinformatics
• Computational Biology

Background:

• Pairwise alignment of 3D protein structures is crucial for understanding evolutionary and functional relationships.
• Existing tools lack user-friendly, browser-based interfaces for integrated 1D sequence and 3D structure visualization.

Purpose of the Study:

• To introduce a novel, user-friendly, browser-based tool for pairwise protein structure alignment.
• To facilitate the visualization of alignments at both 1D sequence and 3D structural levels.

Main Methods:

• Integration with the RCSB Protein Data Bank (RCSB PDB) web portal (rcsb.org/alignment).
• Support for multiple alignment algorithms (FATCAT, CE, TM-align, Smith-Waterman 3D).
• Visualization using RCSB PDB Sequence Annotations viewer and Mol* 3D viewer.

Main Results:

• Seamless integration into RCSB.org, offering programmatic access via alignment.rcsb.org.
• Rapid alignment of protein chains against reference structures, including PDB archive and Computed Structure Models.
• User-friendly interface for parameter setup, input selection, and visualization of 1D and 3D results.
• Ability to align custom structure data via URL or file upload.
• Bookmarking and sharing of alignment results.

Conclusions:

• The novel alignment tool bridges the gap between 1D sequence and 3D protein structures.
• Facilitates deeper understanding of complex evolutionary relationships through comprehensive analyses.
• Enhances structural biology and bioinformatics research by providing an accessible and integrated alignment solution.