ArticleNucleic acids research2018
ChannelsDB: database of biomacromolecular tunnels and pores.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- ChannelsDB 2.0: a comprehensive database of protein tunnels and pores in AlphaFold era.Nucleic acids research · 2024Article
- Analysis and Visualization of Protein Channels, Tunnels, and Pores with MOLEonline and ChannelsDB 2.0.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Understanding Life at High Temperatures: Relationships of Molecular Channels in Enzymes of Methanogenic Archaea and Their Growth Temperatures.International journal of molecular sciences · 2022Article
- PDBe and PDBe-KB: Providing high-quality, up-to-date and integrated resources of macromolecular structures to support basic and applied research and education.Protein science : a publication of the Protein Society · 2022Article
- Worldwide Protein Data Bank (wwPDB): A virtual treasure for research in biotechnology.European journal of microbiology & immunology · 2022Review
- PDBe-KB: collaboratively defining the biological context of structural data.Nucleic acids research · 2022Article
- ChanFAD: A Functional Annotation Database for Ion Channels.Frontiers in bioinformatics · 2022Article
- Structural Characterization of Multienzyme Assemblies: An Overview.Methods in molecular biology (Clifton, N.J.) · 2022Review
- NAChRDB: A Web Resource of Structure-Function Annotations to Unravel the Allostery of Nicotinic Acetylcholine Receptors.ACS omega · 2021Article
- Surface hydrophobics mediate functional dimerization of CYP121A1 of Mycobacterium tuberculosis.Scientific reports · 2021Article
- "Protein" no longer means what it used to.Current research in structural biology · 2021Review
- Crystal Structures of Drug-Metabolizing CYPs.Methods in molecular biology (Clifton, N.J.) · 2021Article
- High-performance macromolecular data delivery and visualization for the web.Acta crystallographica. Section D, Structural biology · 2020Article
- Analysis of protein missense alterations by combining sequence- and structure-based methods.Molecular genetics & genomic medicine · 2020Article
- PDBe-KB: a community-driven resource for structural and functional annotations.Nucleic acids research · 2020Article
- Article
- Coarse-grain simulations on NMR conformational ensembles highlight functional residues in proteins.Journal of the Royal Society, Interface · 2019Article
- Differences in the path to exit the ribosome across the three domains of life.Nucleic acids research · 2019Article
- Molecular Tunnels in Enzymes and Thermophily: A Case Study on the Relationship to Growth Temperature.Microorganisms · 2018Article
- MOLEonline: a web-based tool for analyzing channels, tunnels and pores (2018 update).Nucleic acids research · 2018Article
Corrections and comments
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.