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MOLEonline 2.0: interactive web-based analysis of biomacromolecular channels

K. Berka, O. Hanak, D. Sehnal, P. Banas, V. Navratilova, D. Jaiswal, C.-M. Ionescu, R. Svobodova Varekova, J. Koca, M. Otyepka
2012 Nucleic Acids Research  
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.  ...  CONCLUSIONS In this article, we described MOLEonline 2.0 (http://ncbr or, a new web-based interactive tool for the analysis of molecular channels and pores.  ... 
doi:10.1093/nar/gks363 pmid:22553366 pmcid:PMC3394309 fatcat:6va5wncwirfonmo4l4j2vsztgm

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

Lukáš Pravda, David Sehnal, Dominik Toušek, Veronika Navrátilová, Václav Bazgier, Karel Berka, Radka Svobodová Vařeková, Jaroslav Koča, Michal Otyepka
2018 Nucleic Acids Research  
MOLEonline is an interactive, web-based application for the detection and characterization of channels (pores and tunnels) within biomacromolecular structures.  ...  The application enables two modes of calculation: one is dedicated to the analysis of channels while the other was specifically designed for transmembrane pores.  ...  The figure was generated in Pymol software (31) from a MOLEonline report. of channel analysis are available on the MOLEonline web page (  ... 
doi:10.1093/nar/gky309 pmid:29718451 pmcid:PMC6030847 fatcat:6ghhwqjhqfefjdntqb3jom34ju

MOLE 2.0: advanced approach for analysis of biomacromolecular channels

David Sehnal, Radka Svobodová Vařeková, Karel Berka, Lukáš Pravda, Veronika Navrátilová, Pavel Banáš, Crina-Maria Ionescu, Michal Otyepka, Jaroslav Koča
2013 Journal of Cheminformatics  
As a new feature, MOLE 2.0 estimates physicochemical properties of the identified channels, i.e., hydropathy, hydrophobicity, polarity, charge, and mutability.  ...  Thus, the predicted physicochemical properties may provide useful information about the potential functions of identified channels. The MOLE 2.0 software is available at  ...  Some functionality is also available in a platform-independent manner via the web-based application MOLEonline 2.0 [41] .  ... 
doi:10.1186/1758-2946-5-39 pmid:23953065 pmcid:PMC3765717 fatcat:qdyxgiwt6nhazjkvzmwqe4hi6a