Analysis and Visualization of Protein Channels, Tunnels, and Pores with MOLEonline and ChannelsDB 2.0
Language English Country United States Media print
Document type Journal Article
- Keywords
- Biomacromolecule, PDB, Physicochemical properties, Pore, Protein, Residues, Tunnel, Visualization, Voronoi, mmCIF, Channel,
- MeSH
- Databases, Protein * MeSH
- Web Browser MeSH
- Ion Channels metabolism chemistry MeSH
- Protein Conformation MeSH
- Models, Molecular MeSH
- Proteins chemistry metabolism MeSH
- Software * MeSH
- User-Computer Interface MeSH
- Computational Biology methods MeSH
- Publication type
- Journal Article MeSH
- Names of Substances
- Ion Channels MeSH
- Proteins MeSH
Channels, tunnels, and pores serve as pathways for the transport of molecules and ions through protein structures, thus participating to their functions. MOLEonline ( https://mole.upol.cz ) is an interactive web-based tool with enhanced capabilities for detecting and characterizing channels, tunnels, and pores within protein structures. MOLEonline has two distinct calculation modes for analysis of channel and tunnels or transmembrane pores. This application gives researchers rich analytical insights into channel detection, structural characterization, and physicochemical properties. ChannelsDB 2.0 ( https://channelsdb2.biodata.ceitec.cz/ ) is a comprehensive database that offers information on the location, geometry, and physicochemical characteristics of tunnels and pores within macromolecular structures deposited in Protein Data Bank and AlphaFill databases. These tunnels are sourced from manual deposition from literature and automatic detection using software tools MOLE and CAVER. MOLEonline and ChannelsDB visualization is powered by the LiteMol Viewer and Mol* viewer, ensuring a user-friendly workspace. This chapter provides an overview of user applications and usage.
Central European Institute of Technology Masaryk University Brno Brno Czech Republic
Faculty of Science National Centre for Biomolecular Research Brno Czech Republic
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