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

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00159816%3A_____%2F24%3A00079726" target="_blank" >RIV/00159816:_____/24:00079726 - isvavai.cz</a>

Nalezeny alternativní kódy

RIV/00216224:14310/24:00135278 RIV/61989592:15310/24:73620930

Výsledek na webu

<a href="https://academic.oup.com/nar/article/52/D1/D413/7416806" target="_blank" >https://academic.oup.com/nar/article/52/D1/D413/7416806</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1093/nar/gkad1012" target="_blank" >10.1093/nar/gkad1012</a>

Jazyk výsledku

angličtina

Název v původním jazyce

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

Popis výsledku v původním jazyce

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. Graphical Abstract

Název v anglickém jazyce

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

Popis výsledku anglicky

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. Graphical Abstract

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

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OECD FORD obor

10608 - Biochemistry and molecular biology

Projekt

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

Návaznosti

—

Rok uplatnění

2024

Kód důvěrnosti údajů

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

Název periodika

Nucleic Acids Research

ISSN

0305-1048

e-ISSN

1362-4962

Svazek periodika

52

Číslo periodika v rámci svazku

D1

Stát vydavatele periodika

US - Spojené státy americké

Počet stran výsledku

6

Strana od-do

"D413"-"D418"

Kód UT WoS článku

001101754200001

EID výsledku v databázi Scopus

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