SUMMARY: MOLEonline is an interactive, web-based tool designed to detect and analyse channels (pores and tunnels) within protein structures. The latest version of MOLEonline addresses the limitations of its predecessor by integrating the Mol* viewer for visualization and offering a streamlined, fully interactive user experience. The new features include colouring tunnels in the 3D viewer based on their physicochemical properties. A 2D representation of the protein structure and calculated tunnels is generated using 2DProts. Users can now store tunnels directly in the mmCIF file format, facilitating sharing via the community-standard FAIR format for structural data. In addition, the ability to store and load computation settings ensures the reproducibility of tunnel computation results. Integration with the ChannelsDB 2.0 database allows users to access precomputed tunnels. AVAILABILITY AND IMPLEMENTATION: The MOLEonline application is freely available at https://moleonline.cz with no login requirement, its source code is stored at GitHub under the MIT licence at https://github.com/sb-ncbr/moleonline-web, and archived at Figshare at https://doi.org/10.6084/m9.figshare.29816174.

• MeSH
• Databases, Protein MeSH
• Internet MeSH
• Protein Conformation MeSH
• Proteins * chemistry   MeSH
• Software * MeSH
• User-Computer Interface MeSH
• Computational Biology * methods   MeSH
• Publication type
• Journal Article MeSH
• Names of Substances
• 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.

• 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

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.

• MeSH
• Amino Acids MeSH
• Databases, Protein * MeSH
• Protein Conformation MeSH
• Proteins * chemistry   MeSH
• Software * MeSH
• Publication type
• Journal Article MeSH
• Names of Substances
• Amino Acids MeSH
• Proteins * MeSH

Caver Web 1.0 is a web server for comprehensive analysis of protein tunnels and channels, and study of the ligands' transport through these transport pathways. Caver Web is the first interactive tool allowing both the analyses within a single graphical user interface. The server is built on top of the abundantly used tunnel detection tool Caver 3.02 and CaverDock 1.0 enabling the study of the ligand transport. The program is easy-to-use as the only required inputs are a protein structure for a tunnel identification and a list of ligands for the transport analysis. The automated guidance procedures assist the users to set up the calculation in a way to obtain biologically relevant results. The identified tunnels, their properties, energy profiles and trajectories for ligands' passages can be calculated and visualized. The tool is very fast (2-20 min per job) and is applicable even for virtual screening purposes. Its simple setup and comprehensive graphical user interface make the tool accessible for a broad scientific community. The server is freely available at https://loschmidt.chemi.muni.cz/caverweb.

• MeSH
• Algorithms * MeSH
• Benchmarking MeSH
• Protein Interaction Domains and Motifs MeSH
• Internet MeSH
• Protein Structure, Quaternary MeSH
• Humans MeSH
• Ligands MeSH
• Amino Acid Sequence MeSH
• Molecular Docking Simulation MeSH
• Protein Structure, Tertiary MeSH
• Carrier Proteins chemistry   metabolism   MeSH
• User-Computer Interface * MeSH
• Protein Binding MeSH
• Binding Sites MeSH
• Computational Biology methods   MeSH
• Animals MeSH
• Check Tag
• Humans MeSH
• Animals MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Names of Substances
• Ligands MeSH
• Carrier Proteins MeSH