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Abstract MotivationTools for pairwise alignments between 3D structures of proteins are of fundamental importance for structural biology and bioinformatics, enabling visual exploration of evolutionary and functional relationships. However, the absence of a user-friendly, browser-based tool for creating alignments and visualizing them at both 1D sequence and 3D structural levels makes this process unnecessarily cumbersome. ResultsWe introduce a novel pairwise structure alignment tool (rcsb.org/alignment) that seamlessly integrates into the RCSB Protein Data Bank (RCSB PDB) research-focused RCSB.org web portal. Our 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). The user-friendly interface simplifies parameter setup and input selection. Within seconds, our tool enables visualization of results in both sequence (1D) and structural (3D) perspectives through the RCSB PDB RCSB.org Sequence Annotations viewer and Mol* 3D viewer, respectively. 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. Moreover, this tool can 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, our tool facilitates deeper understanding of complex evolutionary relationships among proteins through comprehensive sequence and structural analyses. Availability and implementationThe alignment tool is part of the RCSB PDB research-focused RCSB.org web portal and available at rcsb.org/alignment. Programmatic access is available via alignment.rcsb.org. Frontend code has been published at github.com/rcsb/rcsb-pecos-app. Visualization is powered by the open-source Mol* viewer (github.com/molstar/molstar and github.com/molstar/rcsb-molstar) plus the Sequence Annotations in 3D Viewer (github.com/rcsb/rcsb-saguaro-3d). 

Abstract The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB, RCSB.org), the US Worldwide Protein Data Bank (wwPDB, wwPDB.org) data center for the global PDB archive, provides access to the PDB data via its RCSB.org research-focused web portal. We report substantial additions to the tools and visualization features available at RCSB.org, which now delivers more than 227000 experimentally determined atomic-level three-dimensional (3D) biostructures stored in the global PDB archive alongside more than 1 million Computed Structure Models (CSMs) of proteins (including models for human, model organisms, select human pathogens, crop plants and organisms important for addressing climate change). In addition to providing support for 3D structure motif searches with user-provided coordinates, new features highlighted herein include query results organized by redundancy-reduced Groups and summary pages that facilitate exploration of groups of similar proteins. Newly released programmatic tools are also described, as are enhanced training opportunities.