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.

CEITEC Central European Institute of Technology Masaryk University Kamenice 5 625 00 Brno Czech Republic

Department of Physical Chemistry Faculty of Science Palacký University 17 listopadu 1192 12 771 46 Olomouc Czech Republic

National Centre for Biomolecular Research Faculty of Science Masaryk University Kamenice 5 625 00 Brno Czech Republic

See more in PubMed

Ayub M, Bayley H.  Engineered transmembrane pores. Curr Opin Chem Biol  2016;34:117–26. 10.1016/j.cbpa.2016.08.005 PubMed DOI PMC

Chovancova E, Pavelka A, Benes P  et al.  CAVER 3.0: a tool for the analysis of transport pathways in dynamic protein structures. PLoS Comput Biol  2012;8:e1002708. 10.1371/journal.pcbi.1002708 PubMed DOI PMC

Furnham N, Holliday GL, De Beer TA  et al.  The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues identified in enzymes. Nucleic Acids Res  2014;42:D485–9. 10.1093/nar/gkt1243 PubMed DOI PMC

Hekkelman ML, de Vries I, Joosten RP  et al.  AlphaFill: enriching AlphaFold models with ligands and cofactors. Nat Methods  2023;20:205–13. 10.1038/s41592-022-01685-y PubMed DOI PMC

Hille B.  Ionic channels in nerve membranes, 50 years on. Prog Biophys Mol Biol  2022;169–170:12–20. 10.1016/j.pbiomolbio.2021.11.003 PubMed DOI PMC

Hu H, Ataka K, Menny A  et al.  Electrostatics, proton sensor, and networks governing the gating transition in GLIC, a proton-gated pentameric ion channel. Proc Natl Acad Sci USA  2018;115:E12172–81. 10.1073/pnas.1813378116 PubMed DOI PMC

Hutařová Vařeková I, Hutař J, Midlik A  et al.  2DProts: database of family-wide protein secondary structure diagrams. Bioinformatics  2021;37:4599–601. 10.1093/bioinformatics/btab505 PubMed DOI PMC

Kokkonen P, Bednar D, Pinto G  et al.  Engineering enzyme access tunnels. Biotechnol Adv  2019;37:107386. 10.1016/j.biotechadv.2019.04.008 PubMed DOI

Marques SM, Daniel L, Buryska T  et al.  Enzyme tunnels and gates as relevant targets in drug design. Med Res Rev  2017;37:1095–139. 10.1002/med.21430 PubMed DOI

Midlik A, Navrátilová V, Moturu TR  et al.  Uncovering of cytochrome P450 anatomy by SecStrAnnotator. Sci Rep  2021;11:12345. 10.1038/s41598-021-91494-8 PubMed DOI PMC

Nugent T, Jones DT.  Membrane protein orientation and refinement using a knowledge-based statistical potential. BMC Bioinformatics  2013;14:276–10. 10.1186/1471-2105-14-276 PubMed DOI PMC

Perez-Zoghbi JF, Karner C, Ito S  et al.  Ion channel regulation of intracellular calcium and airway smooth muscle function. Pulm Pharmacol Ther  2009;22:388–97. 10.1016/j.pupt.2008.09.006 PubMed DOI PMC

Pravda L, Berka K, Svobodová Vařeková R  et al.  Anatomy of enzyme channels. BMC Bioinformatics  2014;15:379. 10.1186/s12859-014-0379-x PubMed DOI PMC

Pravda L, Sehnal D, Toušek D  et al.  MOLEonline: a web-based tool for analyzing channels, tunnels and pores (2018 update). Nucleic Acids Res  2018;46:W368–73. 10.1093/nar/gky309 PubMed DOI PMC

Sauguet L, Shahsavar A, Delarue M.  Crystallographic studies of pharmacological sites in pentameric ligand-gated ion channels. Biochim Biophys Acta  2015;1850:511–23. 10.1016/j.bbagen.2014.05.007 PubMed DOI

Schoch GA, Yano JK, Sansen S  et al.  Determinants of cytochrome P450 2C8 substrate binding: structures of complexes with montelukast, troglitazone, felodipine, and 9-cis-retinoic acid. J Biol Chem  2008;283:17227–37. 10.1074/jbc.M802180200 PubMed DOI PMC

Sehnal D, Svobodová Vařeková R, Berka K  et al.  MOLE 2.0: advanced approach for analysis of biomacromolecular channels. J Cheminform  2013;5:39. 10.1186/1758-2946-5-39 PubMed DOI PMC

Sehnal D, Deshpande M, Vařeková RS  et al.  LiteMol suite: interactive web-based visualization of large-scale macromolecular structure data. Nat Methods  2017;14:1121–2. 10.1038/nmeth.4499 PubMed DOI

Sehnal D, Bittrich S, Deshpande M  et al.  Mol Viewer: modern web app for 3D visualization and analysis of large biomolecular structures. Nucleic Acids Res  2021;49:W431–7. 10.1093/nar/gkab314 PubMed DOI PMC

Sillitoe I, Bordin N, Dawson N  et al.  CATH: increased structural coverage of functional space. Nucleic Acids Res  2021;49:D266–73. 10.1093/nar/gkaa1079 PubMed DOI PMC

Špačková A, Vávra O, Raček T  et al.  ChannelsDB 2.0: a comprehensive database of protein tunnels and pores in AlphaFold era. Nucleic Acids Res  2024;52:D413–8. 10.1093/nar/gkad1012 PubMed DOI PMC

Stourac J, Vavra O, Kokkonen P  et al.  Caver Web 1.0: identification of tunnels and channels in proteins and analysis of ligand transport. Nucleic Acids Res  2019;47:W414–22. 10.1093/nar/gkz378 PubMed DOI PMC

Vavra O, Filipovic J, Plhak J  et al.  CaverDock: a molecular docking-based tool to analyse ligand transport through protein tunnels and channels. Bioinformatics  2019;35:4986–93. 10.1093/bioinformatics/btz386 PubMed DOI

Vavra O, Tyzack J, Haddadi F  et al.  Large-scale annotation of biochemically relevant pockets and tunnels in cognate enzyme–ligand complexes. J Cheminform  2024;16:114. 10.1186/s13321-024-00907-z PubMed DOI PMC