MOLEonline: a web-based tool for analyzing channels, tunnels and pores (2018 update). Issue Volume 46:Issue W1(2018) (30th April 2018)

• Record Type: Journal Article
• Authors: Pravda, Lukáš; Sehnal, David; Toušek, Dominik; Navrátilová, Veronika; Bazgier, Václav; Berka, Karel; Svobodová Vařeková, Radka; Koča, Jaroslav; Otyepka, Michal
• Is Part Of: Nucleic acids research. Volume 46:Issue W1(2018)
• Page Start: W368
• Page End: W373
• Publication Date: 2018-04-30
• Subjects: Nucleic acids -- Periodicals; Molecular biology -- Periodicals; 572.805
• DOI: 10.1093/nar/gky309
• Languages: English
• ISSNs: 0305-1048

Abstract

Abstract: MOLEonline is an interactive, web-based application for the detection and characterization of channels (pores and tunnels) within biomacromolecular structures. The updated version of MOLEonline overcomes limitations of the previous version by incorporating the recently developed LiteMol Viewer visualization engine and providing a simple, fully interactive user experience. The application enables two modes of calculation: one is dedicated to the analysis of channels while the other was specifically designed for transmembrane pores. As the application can use both PDB and mmCIF formats, it can be leveraged to analyze a wide spectrum of biomacromolecular structures, e.g. stemming from NMR, X-ray and cryo-EM techniques. The tool is interconnected with other bioinformatics tools (e.g., PDBe, CSA, ChannelsDB, OPM, UniProt) to help both setup and the analysis of acquired results. MOLEonline provides unprecedented analytics for the detection and structural characterization of channels, as well as information about their numerous physicochemical features. Here we present the application of MOLEonline for structural analyses of α-hemolysin and transient receptor potential mucolipin 1 (TRMP1) pores. The MOLEonline application is freely available via the Internet at https://mole.upol.cz .