ArticleNucleic acids research2024
AlphaFind: discover structure similarity across the proteome in AlphaFold DB.
Article in Nucleic acids research, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- AlphaFind v2: similarity search in AlphaFold DB and TED domains across structural contexts.Nucleic acids research · 2026Article
- MolViewStories: Interactive molecular storytelling.Protein science : a publication of the Protein Society · 2026Article
- An interpretable alphabet for local protein structure search based on amino acid neighborhoods.Bioinformatics (Oxford, England) · 2025Article
- Advances of deep Neural Networks (DNNs) in the development of peptide drugs.Future medicinal chemistry · 2025Review
- Fast protein structure searching using structure graph embeddings.Bioinformatics advances · 2025Article
- Engineering conditional protein-protein interactions for dynamic cellular control.Biotechnology advances · 2024Review
- Review
- RCSB protein Data Bank: exploring protein 3D similarities via comprehensive structural alignments.Bioinformatics (Oxford, England) · 2024Article
Corrections and comments
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Authors and funding
11 authors.
Funding
Abstract
AlphaFind is a web-based search engine that provides fast structure-based retrieval in the entire set of AlphaFold DB structures. Unlike other protein processing tools, AlphaFind is focused entirely on tertiary structure, automatically extracting the main 3D features of each protein chain and using a machine learning model to find the most similar structures. This indexing approach and the 3D feature extraction method used by AlphaFind have both demonstrated remarkable scalability to large datasets as well as to large protein structures. The web application itself has been designed with a focus on clarity and ease of use. The searcher accepts any valid UniProt ID, Protein Data Bank ID or gene symbol as input, and returns a set of similar protein chains from AlphaFold DB, including various similarity metrics between the query and each of the retrieved results. In addition to the main search functionality, the application provides 3D visualizations of protein structure superpositions in order to allow researchers to instantly analyze the structural similarity of the retrieved results. The AlphaFind web application is available online for free and without any registration at https://alphafind.fi.muni.cz.
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Registered trials
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