ArticlePLoS computational biology2020
Real-time structural motif searching in proteins using an inverted index strategy.
Article in PLoS computational biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
- Iterative and data-driven ortholog mining enables reliable discovery of stereoselective ketoreductases.Nature communications · 2026Article
- Investigating enzyme function by geometric matching of catalytic motifs.Protein science : a publication of the Protein Society · 2026Article
- RCSB protein data Bank: Next-generation advanced search for exploration of experimental structures and computed structure models.Protein science : a publication of the Protein Society · 2026Article
- Zero-shot design of abioRxiv : the preprint server for biology · 2026Article
- Structural motif search across the protein universe with Folddisco.Nature biotechnology · 2026Article
- Interpretable prediction of zinc ion location in proteins with ZincSight.Protein science : a publication of the Protein Society · 2025Article
- ActSeek: fast and accurate search algorithm of active sites in alphafold database.Bioinformatics (Oxford, England) · 2025Article
- rcsb-api: Python Toolkit for Streamlining Access to RCSB Protein Data Bank APIs.Journal of molecular biology · 2025Article
- Insights into a water-mediated catalytic triad architecture in CE20 carbohydrate esterases.Nature communications · 2025Article
- ProteinsPlus: a publicly available resource for protein structure mining.Nucleic acids research · 2025Article
- Role of Active Site Residues and Weak Noncovalent Interactions in Substrate Positioning inBiochemistry · 2025Article
- Cross-reactive sarbecovirus antibodies induced by mosaic RBD nanoparticles.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Advanced glycation end product (AGE) crosslinking of a bacterial protein: Are AGE-modifications going undetected in our studies?Structural dynamics (Melville, N.Y.) · 2025Article
- Cross-reactive sarbecovirus antibodies induced by mosaic RBD-nanoparticles.bioRxiv : the preprint server for biology · 2025Article
- Visualizing and analyzing 3D biomolecular structures using Mol* at RCSB.org: Influenza A H5N1 virus proteome case study.Protein science : a publication of the Protein Society · 2025Article
- Long-Range Electrostatics in Serine Proteases: Machine Learning-Driven Reaction Sampling Yields Insights for Enzyme Design.Journal of chemical information and modeling · 2025Article
- The metal cofactor: stationary or mobile?Applied microbiology and biotechnology · 2024Review
- User-centric design of a 3D search interface for protein-ligand complexes.Journal of computer-aided molecular design · 2024Article
- Article
- Dual-wield NTPases: A novel protein family mined from AlphaFold DB.Protein science : a publication of the Protein Society · 2024Article
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3 authors.
Funding
Abstract
Biochemical and biological functions of proteins are the product of both the overall fold of the polypeptide chain, and, typically, structural motifs made up of smaller numbers of amino acids constituting a catalytic center or a binding site that may be remote from one another in amino acid sequence. Detection of such structural motifs can provide valuable insights into the function(s) of previously uncharacterized proteins. Technically, this remains an extremely challenging problem because of the size of the Protein Data Bank (PDB) archive. Existing methods depend on a clustering by sequence similarity and can be computationally slow. We have developed a new approach that uses an inverted index strategy capable of analyzing >170,000 PDB structures with unmatched speed. The efficiency of the inverted index method depends critically on identifying the small number of structures containing the query motif and ignoring most of the structures that are irrelevant. Our approach (implemented at motif.rcsb.org) enables real-time retrieval and superposition of structural motifs, either extracted from a reference structure or uploaded by the user. Herein, we describe the method and present five case studies that exemplify its efficacy and speed for analyzing 3D structures of both proteins and nucleic acids.
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