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.

Biological Data Management and Analysis Core Facility CEITEC Central European Institute of Technology Masaryk University Studentská Brno 62500 Czech Republic

Faculty of Informatics Masaryk University Botanická 68A Brno 60200 Czech Republic

Institute of Computer Science Masaryk University Šumavská 416 15 Brno 60200 Czech Republic

National Centre for Biomolecular Research Faculty of Science Masaryk University Kamenice 5 Brno 62500 Czech Republic

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