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

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

2024 | Sebastian Bittrich, Joan Segura, Jose M. Duarte, Stephen K. Burley, Yana Rose
The RCSB Protein Data Bank (RCSB PDB) has introduced a novel pairwise structure alignment tool (rcsb.org/alignment) that integrates seamlessly into the RCSB.org web portal. This tool, accessible via the application programming interface (API, alignment.rcsb.org), enables users to align multiple protein chains with a reference structure using established alignment algorithms such as FATCA, CE, TM-align, or Smith-Waterman 3D. The user-friendly interface simplifies parameter setup and input selection, allowing users to visualize results in both sequence (1D) and structural (3D) perspectives through the RCSB PDB's Sequence Annotations viewer and Mol* 3D viewer. The tool supports various file formats and external URLs, and alignment results can be bookmarked and shared. This comprehensive approach facilitates deeper understanding of evolutionary relationships among proteins through sequence and structural analyses. The tool is part of the RCSB PDB's efforts to enhance the accessibility and utility of protein structure data, particularly in the context of machine learning-based structure predictions from sources like AlphaFold DB and ModelArchive.The RCSB Protein Data Bank (RCSB PDB) has introduced a novel pairwise structure alignment tool (rcsb.org/alignment) that integrates seamlessly into the RCSB.org web portal. This tool, accessible via the application programming interface (API, alignment.rcsb.org), enables users to align multiple protein chains with a reference structure using established alignment algorithms such as FATCA, CE, TM-align, or Smith-Waterman 3D. The user-friendly interface simplifies parameter setup and input selection, allowing users to visualize results in both sequence (1D) and structural (3D) perspectives through the RCSB PDB's Sequence Annotations viewer and Mol* 3D viewer. The tool supports various file formats and external URLs, and alignment results can be bookmarked and shared. This comprehensive approach facilitates deeper understanding of evolutionary relationships among proteins through sequence and structural analyses. The tool is part of the RCSB PDB's efforts to enhance the accessibility and utility of protein structure data, particularly in the context of machine learning-based structure predictions from sources like AlphaFold DB and ModelArchive.
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[slides and audio] RCSB protein Data Bank%3A exploring protein 3D similarities via comprehensive structural alignments