ChannelsDB


37956324	ChannelsDB 2.0: a comprehensive database of protein tunnels and pores in AlphaFold era. [PMID: 37956324] Anna Špačková, Ondřej Vávra, Tomáš Raček, Václav Bazgier, David Sehnal, Jiří Damborský, Radka Svobodová, David Bednář, Karel Berka Abstract 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 ∼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. Nucleic Acids Res. 2024:52(D1) \| 5 Citations (from Europe PMC, 2025-04-05)
29036719	ChannelsDB: database of biomacromolecular tunnels and pores. [PMID: 29036719] Pravda L, Sehnal D, Svobodová Vareková R, Navrátilová V, Toušek D, Berka K, Otyepka M, Koca J. Abstract ChannelsDB (http://ncbr.muni.cz/ChannelsDB) is a database providing information about the positions, geometry and physicochemical properties of channels (pores and tunnels) found within biomacromolecular structures deposited in the Protein Data Bank. Channels were deposited from two sources; from literature using manual deposition and from a software tool automatically detecting tunnels leading to the enzymatic active sites and selected cofactors, and transmembrane pores. The database stores information about geometrical features (e.g. length and radius profile along a channel) and physicochemical properties involving polarity, hydrophobicity, hydropathy, charge and mutability. The stored data are interlinked with available UniProt annotation data mapping known mutation effects to channel-lining residues. All structures with channels are displayed in a clear interactive manner, further facilitating data manipulation and interpretation. As such, ChannelsDB provides an invaluable resource for research related to deciphering the biological function of biomacromolecular channels. Nucleic Acids Res. 2018:46(D1) \| 21 Citations (from Europe PMC, 2025-04-05)

ChannelsDB 2.0: a comprehensive database of protein tunnels and pores in AlphaFold era. [PMID: 37956324]

Anna Špačková, Ondřej Vávra, Tomáš Raček, Václav Bazgier, David Sehnal, Jiří Damborský, Radka Svobodová, David Bednář, Karel Berka

Abstract

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 ∼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.

Nucleic Acids Res. 2024:52(D1) | 5 Citations (from Europe PMC, 2025-04-05)

ChannelsDB: database of biomacromolecular tunnels and pores. [PMID: 29036719]

Pravda L, Sehnal D, Svobodová Vareková R, Navrátilová V, Toušek D, Berka K, Otyepka M, Koca J.

Abstract

ChannelsDB (http://ncbr.muni.cz/ChannelsDB) is a database providing information about the positions, geometry and physicochemical properties of channels (pores and tunnels) found within biomacromolecular structures deposited in the Protein Data Bank. Channels were deposited from two sources; from literature using manual deposition and from a software tool automatically detecting tunnels leading to the enzymatic active sites and selected cofactors, and transmembrane pores. The database stores information about geometrical features (e.g. length and radius profile along a channel) and physicochemical properties involving polarity, hydrophobicity, hydropathy, charge and mutability. The stored data are interlinked with available UniProt annotation data mapping known mutation effects to channel-lining residues. All structures with channels are displayed in a clear interactive manner, further facilitating data manipulation and interpretation. As such, ChannelsDB provides an invaluable resource for research related to deciphering the biological function of biomacromolecular channels.

Nucleic Acids Res. 2018:46(D1) | 21 Citations (from Europe PMC, 2025-04-05)

URL:	https://channelsdb2.biodata.ceitec.cz/
Full name:	ChannelsDB
Description:	ChannelsDB 2.0 is a comprehensive and regularly updated resource of channels, pores and tunnels found in biomacromolecules deposited in the Protein Data Bank and AlphaFill / AlphaFold databases. As such, it is a unique service for channel-related analyses. Pathways were calculated using an algorithms CAVER and MOLE.
Year founded:	2018
Last update:	2018
Version:	v2.0
Accessibility:	Accessible
Country/Region:	Czech Republic

Data type:	Other
Data object:	Animal Bacteria
Database category:	Gene genome and annotation Standard ontology and nomenclature
Major species:	Homo sapiens
Keywords:	geometrical features physicochemical properties

University/Institution:	Central European Institute of Technology
Address:	CEITEC - Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno-Bohunice, Czech Republic National Centre for Biomolecular Research, Faculty of Science, Kamenice 5, 625 00 Brno-Bohunice, Czech Republic Tel: +420 549492685; Fax: +420 549491060
City:
Province/State:
Country/Region:	Czech Republic
Contact name (PI/Team):	Jaroslav Koča
Contact email (PI/Helpdesk):	jaroslav.koca@ceitec.muni.cz

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