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Paper Published: Exploring protein 3D similarities via comprehensive structural alignments
08/27 
Figure 1: Output of the pairwise alignment application.
(2024) Bioinformatics 40: btae370 doi: 10.1093/bioinformatics/btae370
This article introduces a novel pairwise structure alignment tool (rcsb.org/alignment) that seamlessly integrates into RCSB.org. The tool and its underlying application programming interface (alignment.rcsb.org) empowers users to align several protein chains with a reference structure by providing access to established alignment algorithms (FATCAT, CE, TM-align, or Smith–Waterman 3D).
Users can effortlessly compare structures deposited in the PDB archive alongside more than a million incorporated Computed Structure Models coming from the ModelArchive and AlphaFold DB.
This tool can also be used to align custom structure data by providing a link/URL or uploading atomic coordinate files directly. Importantly, alignment results can be bookmarked and shared with collaborators.
By bridging the gap between 1D sequence and 3D structures of proteins, this tool facilitates deeper understanding of complex evolutionary relationships among proteins through comprehensive sequence and structural analyses.
RCSB Protein Data Bank: exploring protein 3D similarities via comprehensive structural alignments
Sebastian Bittrich, Joan Segura, Jose M Duarte, Stephen K Burley, Yana Rose
(2024) Bioinformatics 40: btae370 doi: 10.1093/bioinformatics/btae370
