ArticleNucleic acids research2024
ChannelsDB 2.0: a comprehensive database of protein tunnels and pores in AlphaFold era.
Article in Nucleic acids research, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Article
- NanoporeDB: a structural resource of multimeric protein nanopores for single-molecule sensing.GigaScience · 2026Article
- Elastic Net Regression to Predict CDK2 Inhibition.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Uricolysis by Arthrobacter globiformis uricase: structural basis for its catalytic activity and thermostability.Acta pharmacologica Sinica · 2025Article
- Identification and classification of ion-channels across the tree of life provide functional insights into understudied CALHM channels.bioRxiv : the preprint server for biology · 2025Article
- MOLEonline: a web-based tool for analysing channels, tunnels, and pores (2025 update).Bioinformatics (Oxford, England) · 2025Article
- PrankWeb 4: a modular web server for protein-ligand binding site prediction and downstream analysis.Nucleic acids research · 2025Article
- Characterization of the Active Enantiomer and Mapping of the Stereospecific Intermolecular Pattern of a Reference P2X7 Allosteric Antagonist.ACS pharmacology & translational science · 2025Article
- Ranking Single Fluorescent Protein-Based Calcium Biosensor Performance by Molecular Dynamics Simulations.Journal of chemical information and modeling · 2025Article
- Navigating Amaryllidaceae alkaloids: bridging gaps and charting biosynthetic territories.Journal of experimental botany · 2025Review
- Pathogenicity patterns in cytochrome P450 family.Bioinformatics advances · 2025Article
- Large-scale annotation of biochemically relevant pockets and tunnels in cognate enzyme-ligand complexes.Journal of cheminformatics · 2024Article
- ProCogGraph: a graph-based mapping of cognate ligand domain interactions.Bioinformatics advances · 2024Article
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9 authors.
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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.
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