V 2024

AlphaFind: Discover structure similarity across the entire known proteome

PROCHÁZKA, David, Terézia SLANINÁKOVÁ, Jaroslav OĽHA, Adrián ROŠINEC, Katarína GREŠOVÁ et. al.

Basic information

Original name

AlphaFind: Discover structure similarity across the entire known proteome

Authors

PROCHÁZKA, David (203 Czech Republic, guarantor, belonging to the institution), Terézia SLANINÁKOVÁ (703 Slovakia, belonging to the institution), Jaroslav OĽHA (703 Slovakia, belonging to the institution), Adrián ROŠINEC (703 Slovakia, belonging to the institution), Katarína GREŠOVÁ (703 Slovakia, belonging to the institution), Miriama JÁNOŠOVÁ (703 Slovakia, belonging to the institution), Jakub ČILLÍK (703 Slovakia, belonging to the institution), Jana PORUBSKÁ (703 Slovakia, belonging to the institution), Radka SVOBODOVÁ (203 Czech Republic, belonging to the institution), Vlastislav DOHNAL (203 Czech Republic, belonging to the institution) and Matej ANTOL (703 Slovakia, belonging to the institution)

Edition

Cold Spring Harbor, USA, 6 pp. N/A, 2024

Publisher

bioRxiv

Other information

Language

English

Type of outcome

Research report

Field of Study

10200 1.2 Computer and information sciences

Country of publisher

Czech Republic

Confidentiality degree

is not subject to a state or trade secret

References:

Organization unit

Faculty of Informatics

DOI

Keywords in English

Protein structure similarity;Learned metric index;Learned indexing;Protein structure search;AlphaFold DB

Tags

Tags

International impact
Changed: 31/3/2025 09:34, Mgr. Eva Špillingová

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, PDB 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
Name: Naučené indexy pro podobností hledání
Investor: Czech Science Foundation, Learned Indexing for Similarity Searching, Lead Agency
LM2023055, research and development project
Name: Česká národní infrastruktura pro biologická data
Investor: Ministry of Education, Youth and Sports of the CR, ELIXIR-CZ: Czech National Infrastructure for Biological Data
MUNI/A/1590/2023, interní kód MU
Name: Využití technik umělé inteligence pro zpracování dat, komplexní analýzy a vizualizaci rozsáhlých dat
Investor: Masaryk University, Using artificial intelligence techniques for data processing, complex analysis and visualization of large-scale data
721/2023, interní kód MU
Name: Prohledávání velkých sad proteinů na základě podobnosti jejich struktur postaveno na učeném metrickém indexu
Investor: CESNET
90254, large research infrastructures
Name: e-INFRA CZ II