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.

Základní údaje

Originální název

AlphaFind: discover structure similarity across the proteome in AlphaFold DB

Autoři

Vydání

Nucleic acids research, Oxford, Oxford University Press, 2024, 0305-1048

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10201 Computer sciences, information science, bioinformatics

Stát vydavatele

Velká Británie a Severní Irsko

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 14.900 v roce 2022

Organizační jednotka

Fakulta informatiky

DOI

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

Klíčová slova anglicky

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

Štítky

AlphaFind, CODA Research Group, DISA, learned index, LMI, protein similarity search

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 18. 5. 2024 21:22, doc. RNDr. Vlastislav Dohnal, Ph.D.

Anotace

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.

Návaznosti

GF23-07040K, projekt VaV

Název: Naučené indexy pro podobností hledání

Investor: Grantová agentura ČR, Naučené indexy pro podobností hledání, Lead agentura

LM2023055, projekt VaV

Název: Česká národní infrastruktura pro biologická data

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, ELIXIR-CZ: Česká národní infrastruktura pro biologická data

90254, velká výzkumná infrastruktura

Název: 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 a Matej ANTOL. AlphaFind: discover structure similarity across the proteome in AlphaFold DB. Nucleic acids research. Oxford: Oxford University Press, 2024, Neuveden, May 15, s. 1-5. ISSN 0305-1048. Dostupné z: 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 = {May 15},
   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 = {Neuveden},
   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  - Neuveden
IS  - May 15
SP  - 1-5
EP  - 1-5
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 a Matej ANTOL. AlphaFind: discover structure similarity across the proteome in AlphaFold DB. \textit{Nucleic acids research}. Oxford: Oxford University Press, 2024, Neuveden, May 15, s.~1-5. ISSN~0305-1048. Dostupné z: https://dx.doi.org/10.1093/nar/gkae397.

Podrobný výpis o publikaci