Detailed Information on Publication Record
2024
AlphaFind: discover structure similarity across the proteome in AlphaFold DB
PROCHÁZKA, David, Terézia SLANINÁKOVÁ, Jaroslav OĽHA, Adrián ROŠINEC, Katarína GREŠOVÁ et. al.Basic information
Original name
AlphaFind: discover structure similarity across the proteome in AlphaFold DB
Authors
PROCHÁZKA, David, Terézia SLANINÁKOVÁ, Jaroslav OĽHA, Adrián ROŠINEC, Katarína GREŠOVÁ, Miriama JÁNOŠOVÁ, Jakub ČILLÍK, Jana PORUBSKÁ, Radka SVOBODOVÁ, Vlastislav DOHNAL and Matej ANTOL
Edition
Nucleic acids research, Oxford, Oxford University Press, 2024, 0305-1048
Other information
Language
English
Type of outcome
Článek v odborném periodiku
Field of Study
10201 Computer sciences, information science, bioinformatics
Country of publisher
United Kingdom of Great Britain and Northern Ireland
Confidentiality degree
není předmětem státního či obchodního tajemství
References:
Impact factor
Impact factor: 14.900 in 2022
Organization unit
Faculty of Informatics
Keywords in English
AlphaFind;Protein similarity search;Structure-based retrieval;Protein tertiary structure;AlphaFold DB;Machine learning
Tags
International impact, Reviewed
Změněno: 20/10/2024 09:19, Mgr. David Procházka
Abstract
V originále
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.
Links
GF23-07040K, research and development project |
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LM2023055, research and development project |
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MUNI/A/1590/2023, interní kód MU |
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90254, large research infrastructures |
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