MOLEonline: a web-based tool for analyzing channels, tunnels and pores (2018 update)

This publication doesn't include Faculty of Arts. It includes Central European Institute of Technology. Official publication website can be found on muni.cz.

Authors

PRAVDA Lukáš SEHNAL David TOUŠEK Dominik NAVRÁTILOVÁ Veronika BAZGIER Václav BERKA Karel SVOBODOVÁ VAŘEKOVÁ Radka KOČA Jaroslav OTYEPKA Michal

Type Article in Periodical
Magazine / Source Nucleic Acids Research
MU Faculty or unit

Central European Institute of Technology

Citation
Doi http://dx.doi.org/10.1093/nar/gky309
Keywords tunnel; pore; aquaporine; protein; MOLE; software
Attached files
Description 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 alpha-hemolysin and transient receptor potential mucolipin 1 (TRMP1) pores.
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