ChannelsDB 2.0: a comprehensive database of protein tunnels and pores in AlphaFold era

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Publikace nespadá pod Ústav výpočetní techniky, ale pod Přírodovědeckou fakultu. Oficiální stránka publikace je na webu muni.cz.
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ŠPAČKOVÁ Anna VÁVRA Ondřej RAČEK Tomáš BAZGIER Václav SEHNAL David DAMBORSKÝ Jiří SVOBODOVÁ Radka BEDNÁŘ David BERKA Karel

Rok publikování 2024
Druh Článek v odborném periodiku
Fakulta / Pracoviště MU

Přírodovědecká fakulta

Citace
www https://doi.org/10.1093/nar/gkad1012
Doi http://dx.doi.org/10.1093/nar/gkad1012
Klíčová slova amino acids; databases; protein; software; biomacromolecules; 3D structure; organelle- and cell-sized models; visualization
Přiložené soubory
Popis ChannelsDB 2.0 is an updated database providing structural information about the position, geometry and physicochemical properties of protein channels-tunnels and pores-within deposited biomacromolecular structures from PDB and AlphaFoldDB databases. The newly deposited information originated from several sources. Firstly, we included data calculated using a popular CAVER tool to complement the data obtained using original MOLE tool for detection and analysis of protein tunnels and pores. Secondly, we added tunnels starting from cofactors within the AlphaFill database to enlarge the scope of the database to protein models based on Uniprot. This has enlarged available channel annotations similar to 4.6 times as of 1 September 2023. The database stores information about geometrical features, e.g. length and radius, and physico-chemical properties based on channel-lining amino acids. The stored data are interlinked with the available UniProt mutation annotation data. ChannelsDB 2.0 provides an excellent resource for deep analysis of the role of biomacromolecular tunnels and pores. The database is available free of charge: https:////channelsdb2.biodata.ceitec.cz.
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