Abstract
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.
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Acknowledgements
This chapter is dedicated to the memory of prof. RNDr. Jaroslav Koča, DrSc.
Acknowledgement is extended to prof. RNDr. Michal Otyepka, Ph.D. for his former contribution to the MOLE and ChannelsDB projects.
We acknowledge support from Ministry of Youth, Education and Sports (MEYS) research infrastructure ELIXIR CZ project LM2023055, Palacký University Olomouc IGA_PrF_2024_017 for A.Š. and Grant Agency of Czech Republic Junior Star project 22-30571M to D.S.
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Špačková, A., Bazgier, V., Raček, T., Sehnal, D., Svobodová, R., Berka, K. (2024). Analysis and Visualization of Protein Channels, Tunnels, and Pores with MOLEonline and ChannelsDB 2.0. In: Lisacek, F. (eds) Protein Bioinformatics. Methods in Molecular Biology, vol 2836. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-4007-4_12
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DOI: https://doi.org/10.1007/978-1-0716-4007-4_12
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