Reproducible experiments with Learned Metric Index Framework

Slanináková, Terézia; Antol, Matej; Oľha, Jaroslav; Dohnal, Vlastislav; Ladra, Susana; Martínez‐Prieto, Miguel A.

doi:10.1016/j.is.2023.102255

Cited by 3 publications

(1 citation statement)

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“…The application's source code is accessible under the MIT license at https://github.com/Coda-Research-Group/AlphaFind and is also available in the Supplementary Data. The LMI is published and its performance reproducibly examined in (18). The embeddings and weights for the LMI model are available in the Czech National Repository's pilot at https://doi.org/10.48700/datst.d35zf-1ja47.…”

Section: Discussionmentioning

confidence: 99%

AlphaFind: Discover structure similarity across the entire known proteome

Prochazka,

Slaninakova,

Olha

et al. 2024

Preprint

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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.

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Section: Discussionmentioning

confidence: 99%

AlphaFind: Discover structure similarity across the entire known proteome

Prochazka,

Slaninakova,

Olha

et al. 2024

Preprint

Self Cite

View full text Add to dashboard Cite

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SISAP 2023 Indexing Challenge – Learned Metric Index

Slanináková,

Procházka,

Antol

et al. 2023

Lecture Notes in Computer Science

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AlphaFind: discover structure similarity across the proteome in AlphaFold DB

Procházka,

Slanináková,

Olha

et al. 2024

Nucleic Acids Research

Self Cite

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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.

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Reproducible experiments with Learned Metric Index Framework

Cited by 3 publications

References 4 publications

AlphaFind: Discover structure similarity across the entire known proteome

AlphaFind: Discover structure similarity across the entire known proteome

SISAP 2023 Indexing Challenge – Learned Metric Index

AlphaFind: discover structure similarity across the proteome in AlphaFold DB

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