AlphaFind: discover structure similarity across the proteome in AlphaFold DB

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Publikace nespadá pod Fakultu sportovních studií, ale pod Fakultu informatiky. Oficiální stránka publikace je na webu muni.cz.
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PROCHÁZKA David SLANINÁKOVÁ Terézia OĽHA Jaroslav ROŠINEC Adrián GREŠOVÁ Katarína JÁNOŠOVÁ Miriama ČILLÍK Jakub PORUBSKÁ Jana SVOBODOVÁ Radka DOHNAL Vlastislav ANTOL Matej

Rok publikování 2024
Druh Článek v odborném periodiku
Časopis / Zdroj Nucleic acids research
Fakulta / Pracoviště MU

Fakulta informatiky

Citace
www https://doi.org/10.1093/nar/gkae397
Doi http://dx.doi.org/10.1093/nar/gkae397
Klíčová slova AlphaFind;Protein similarity search;Structure-based retrieval;Protein tertiary structure;AlphaFold DB;Machine learning
Popis 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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