Data Exploration Services

Visualization of structure alignments is a valuable tool for the detection of functionally-related positions in proteins, analysis of conformational changes in ligand binding, exploration of structural variation in protein within an evolutionary family, and identification of common structural domains.

A new pairwise structure alignment interface can be used to align a pair of protein chains using the FATCAT, CE, TM-align and Smith-Waterman 3D algorithms. Chains can be easily selected from structures in the PDB structures or from uploaded coordinate files.

Superposed structures will be aligned and launched in the interactive Mol* viewer. Detailed documentation is available. Access the Pairwise Structure Alignment tool from the Analyze menu at the top of the page or directly from RCSB.org/alignment.

Search for Zinc fingers

Structural motif similarities between PDB structures can provide valuable functional and evolutionary insights. A new Structural Motif service finds structures containing a small number of specific amino acids in proximity. This feature looks for residues that appear within 15 Å of each other; the residues may be located far apart in the sequence or appear in different polymer chains.

The search can be launched using the 3D viewer Mol* or through the Advanced Search > Structural Motif option. Help documentation is available.

This service rapidly searches the PDB using the functionality described in Real-time structural motif searching in proteins using an inverted index strategy (2020) PLoS Comput Biol 16(12): e1008502.

A new article in Nucleic Acids Research uses SARS-CoV-2 structures to demonstrate redesigned RCSB.org features for exploring structural data.

RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences

Nucleic Acids Research (2021) 49: D437–D451 doi: 10.1093/nar/gkaa1038

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RCSB PDB team pictured at the January 2020 Cloud Technologies Best Practices hosted by the Institute for Quantitative Biomedicine at Rutgers, The State University of New Jersey.