AlphaFind: Discover structure similarity across the entire known proteome

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14330%2F24%3A00135535" target="_blank" >RIV/00216224:14330/24:00135535 - isvavai.cz</a>

Výsledek na webu

<a href="https://www.biorxiv.org/content/10.1101/2024.02.15.580465v1" target="_blank" >https://www.biorxiv.org/content/10.1101/2024.02.15.580465v1</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1101/2024.02.15.580465" target="_blank" >10.1101/2024.02.15.580465</a>

Jazyk výsledku

angličtina

Název v původním jazyce

AlphaFind: Discover structure similarity across the entire known proteome

Popis výsledku v původním jazyce

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.

Název v anglickém jazyce

AlphaFind: Discover structure similarity across the entire known proteome

Popis výsledku anglicky

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.

Druh

V_souhrn - Souhrnná výzkumná zpráva

CEP obor

—

OECD FORD obor

10200 - Computer and information sciences

Projekt

Výsledek vznikl pri realizaci vícero projektů. Více informací v záložce Projekty.

Návaznosti

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)<br>S - Specificky vyzkum na vysokych skolach

Rok uplatnění

2024

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Počet stran výsledku

6

Místo vydání

Cold Spring Harbor, USA

Název nakladatele resp. objednatele

bioRxiv

Verze

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