AlphaFind: discover structure similarity across the proteome in
AlphaFold DB

J 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 (203 Czech Republic, 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, guarantor, belonging to the institution) and Matej ANTOL (703 Slovakia, belonging to the institution)

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:

URL

Impact factor

Impact factor: 14.900 in 2022

Organization unit

Faculty of Informatics

DOI

http://dx.doi.org/10.1093/nar/gkae397

UT WoS

001222684000001

Keywords in English

AlphaFind;Protein similarity search;Structure-based retrieval;Protein tertiary structure;AlphaFold DB;Machine learning

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

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

90254, large research infrastructures

Name: e-INFRA CZ II

Citovat

PROCHÁZKA, David, Terézia SLANINÁKOVÁ, Jaroslav OĽHA, Adrián ROŠINEC, Katarína GREŠOVÁ, Miriama JÁNOŠOVÁ, Jakub ČILLÍK, Jana PORUBSKÁ, Radka SVOBODOVÁ, Vlastislav DOHNAL and Matej ANTOL. AlphaFind: discover structure similarity across the proteome in AlphaFold DB. Nucleic acids research. Oxford: Oxford University Press, 2024, vol. 52, July 5, p. W182-W186, 5 pp. ISSN 0305-1048. Available from: https://dx.doi.org/10.1093/nar/gkae397.

@article{2402219,
   author = {Procházka, David and Slanináková, Terézia and Oľha, Jaroslav and Rošinec, Adrián and Grešová, Katarína and Jánošová, Miriama and Čillík, Jakub and Porubská, Jana and Svobodová, Radka and Dohnal, Vlastislav and Antol, Matej},
   article_location = {Oxford},
   article_number = {July 5},
   doi = {http://dx.doi.org/10.1093/nar/gkae397},
   keywords = {AlphaFind;Protein similarity search;Structure-based retrieval;Protein tertiary structure;AlphaFold DB;Machine learning},
   language = {eng},
   issn = {0305-1048},
   journal = {Nucleic acids research},
   title = {AlphaFind: discover structure similarity across the proteome in AlphaFold DB},
   url = {https://doi.org/10.1093/nar/gkae397},
   volume = {52},
   year = {2024}
}

TY  - JOUR
ID  - 2402219
AU  - Procházka, David - Slanináková, Terézia - Oľha, Jaroslav - Rošinec, Adrián - Grešová, Katarína - Jánošová, Miriama - Čillík, Jakub - Porubská, Jana - Svobodová, Radka - Dohnal, Vlastislav - Antol, Matej
PY  - 2024
TI  - AlphaFind: discover structure similarity across the proteome in AlphaFold DB
JF  - Nucleic acids research
VL  - 52
IS  - July 5
SP  - W182-W186
EP  - W182-W186
PB  - Oxford University Press
SN  - 03051048
KW  - AlphaFind;Protein similarity search;Structure-based retrieval;Protein tertiary structure;AlphaFold DB;Machine learning
UR  - https://doi.org/10.1093/nar/gkae397
N2  - 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.
ER  -

PROCHÁZKA, David, Terézia SLANINÁKOVÁ, Jaroslav OĽHA, Adrián ROŠINEC, Katarína GREŠOVÁ, Miriama JÁNOŠOVÁ, Jakub ČILLÍK, Jana PORUBSKÁ, Radka SVOBODOVÁ, Vlastislav DOHNAL and Matej ANTOL. AlphaFind: discover structure similarity across the proteome in AlphaFold DB. \textit{Nucleic acids research}. Oxford: Oxford University Press, 2024, vol.~52, July 5, p.~W182-W186, 5 pp. ISSN~0305-1048. Available from: https://dx.doi.org/10.1093/nar/gkae397.

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