title: MOLEonline 2.0: interactive web-based analysis of biomacromolecular channels.
abstract: Biomolecular channels play important roles in many biological systems, e.g. enzymes, ribosomes and ion channels. This article introduces a web-based interactive MOLEonline 2.0 application for the analysis of access/egress paths to interior molecular voids. MOLEonline 2.0 enables platform-independent, easy-to-use and interactive analyses of (bio)macromolecular channels, tunnels and pores. Results are presented in a clear manner, making their interpretation easy. For each channel, MOLEonline displays a 3D graphical representation of the channel, its profile accompanied by a list of lining residues and also its basic physicochemical properties. The users can tune advanced parameters when performing a channel search to direct the search according to their needs. The MOLEonline 2.0 application is freely available via the Internet at http://ncbr.muni.cz/mole or http://mole.upol.cz.
authors.affiliation: Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc, tr. 17. listopadu 12, 771 46 Olomouc, Czech Republic.
authors.forename: Karel
authors.initials: K
authors.lastname: Berka
authors.forename: Ondrej
authors.initials: O
authors.lastname: Hanák
authors.forename: David
authors.initials: D
authors.lastname: Sehnal
authors.forename: Pavel
authors.initials: P
authors.lastname: Banás
authors.forename: Veronika
authors.initials: V
authors.lastname: Navrátilová
authors.forename: Deepti
authors.initials: D
authors.lastname: Jaiswal
authors.forename: Crina-Maria
authors.initials: CM
authors.lastname: Ionescu
authors.forename: Radka
authors.initials: R
authors.lastname: Svobodová Vareková
authors.forename: Jaroslav
authors.initials: J
authors.lastname: Koca
authors.forename: Michal
authors.initials: M
authors.lastname: Otyepka
mesh_terms: D003196:Computer Graphics; D051544:Cytochrome P-450 CYP3A / Q000737:chemistry; D004798:Enzymes / Q000737:chemistry*; D020407:Internet; D007473:Ion Channels / Q000737:chemistry; D008958:Models, Molecular; D011487:Protein Conformation; D054748:Ribosome Subunits, Large, Archaeal / Q000737:chemistry; D012270:Ribosomes / Q000737:chemistry*; D012984:Software; D014584:User-Computer Interface
chemical_list: D004798:Enzymes; D007473:Ion Channels; D051544:Cytochrome P-450 CYP3A