ArticlePloS one2019
RUPEE: A fast and accurate purely geometric protein structure search.
Article in PloS one, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers, 1 of them a synthesis that pooled it.
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Who cites it
23 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Identifying and profiling structural similarities between Spike of SARS-CoV-2 and other viral or host proteins with Machaon.Communications biology · 2023Pooled it
- Prediction of secreted uncharacterized protein structures from Beauveria bassiana ARSEF 2860 unravels novel toxins-like families.Scientific reports · 2025Article
- The proteotranscriptomic characterization of venom in the white seafanOpen biology · 2025Article
- Domainator, a flexible software suite for domain-based annotation and neighborhood analysis, identifies proteins involved in antiviral systems.Nucleic acids research · 2025Article
- Uncovering the potential virulence factors of emerging pathogens using AI/ML-based tools: a case study inFrontiers in cellular and infection microbiology · 2025Article
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- Multi-Omics integration can be used to rescue metabolic information for some of the dark region of the Pseudomonas putida proteome.BMC genomics · 2024Article
- Functional domain annotation by structural similarity.NAR genomics and bioinformatics · 2024Article
- The origin and structural evolution of de novo genes in Drosophila.Nature communications · 2024Article
- In Silico Evaluation, Phylogenetic Analysis, and Structural Modeling of the Class II Hydrophobin Family from Different Fungal Phytopathogens.Microorganisms · 2023Article
- Structure-Function Analysis of RBP7910: An Editosome Z-Binding Protein in Trypanosomatids.Molecules (Basel, Switzerland) · 2023Article
- Novel machine learning approaches revolutionize protein knowledge.Trends in biochemical sciences · 2023Review
- TMEM164 is an acyltransferase that forms ferroptotic C20:4 ether phospholipids.Nature chemical biology · 2023Article
- DPAM: A domain parser for AlphaFold models.Protein science : a publication of the Protein Society · 2023Article
- Prediction of effector protein structures from fungal phytopathogens enables evolutionary analyses.Nature microbiology · 2023Article
- Article
- Vexitoxins: conotoxin-like venom peptides from predatory gastropods of the genusProceedings. Biological sciences · 2022Article
- Unheeded SARS-CoV-2 proteins? A deep look into negative-sense RNA.Briefings in bioinformatics · 2022Article
- Molecular architecture of the human caveolin-1 complex.Science advances · 2022Article
- Are There Hidden Genes in DNA/RNA Vaccines?Frontiers in immunology · 2022Article
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Given the close relationship between protein structure and function, protein structure searches have long played an established role in bioinformatics. Despite their maturity, existing protein structure searches either use simplifying assumptions or compromise between fast response times and quality of results. These limitations can prevent the easy and efficient exploration of relationships between protein structures, which is the norm in other areas of inquiry. To address these limitations we have developed RUPEE, a fast and accurate purely geometric structure search combining techniques from information retrieval and big data with a novel approach to encoding sequences of torsion angles. Comparing our results to the output of mTM, SSM, and the CATHEDRAL structural scan, it is clear that RUPEE has set a new bar for purely geometric big data approaches to protein structure searches. RUPEE in top-aligned mode produces equal or better results than the best available protein structure searches, and RUPEE in fast mode demonstrates the fastest response times coupled with high quality results. The RUPEE protein structure search is available at https://ayoubresearch.com. Code and data are available at https://github.com/rayoub/rupee.
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