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MOLEonline 2.0: interactive web-based analysis of biomacromolecular channels.
Berka K, Hanák O, Sehnal D, Banás P, Navrátilová V, Jaiswal D, Ionescu CM, Svobodová Vareková R, Koca J, Otyepka M. Berka K, et al. Nucleic Acids Res. 2012 Jul;40(Web Server issue):W222-7. doi: 10.1093/nar/gks363. Epub 2012 May 2. Nucleic Acids Res. 2012. PMID: 22553366 Free PMC article.
MOLE 2.0: advanced approach for analysis of biomacromolecular channels.
Sehnal D, Svobodová Vařeková R, Berka K, Pravda L, Navrátilová V, Banáš P, Ionescu CM, Otyepka M, Koča J. Sehnal D, et al. Among authors: berka k. J Cheminform. 2013 Aug 16;5(1):39. doi: 10.1186/1758-2946-5-39. J Cheminform. 2013. PMID: 23953065 Free PMC article.
Anatomy of enzyme channels.
Pravda L, Berka K, Svobodová Vařeková R, Sehnal D, Banáš P, Laskowski RA, Koča J, Otyepka M. Pravda L, et al. Among authors: berka k. BMC Bioinformatics. 2014 Nov 18;15(1):379. doi: 10.1186/s12859-014-0379-x. BMC Bioinformatics. 2014. PMID: 25403510 Free PMC article.
Tools and data services registry: a community effort to document bioinformatics resources.
Ison J, Rapacki K, Ménager H, Kalaš M, Rydza E, Chmura P, Anthon C, Beard N, Berka K, Bolser D, Booth T, Bretaudeau A, Brezovsky J, Casadio R, Cesareni G, Coppens F, Cornell M, Cuccuru G, Davidsen K, Vedova GD, Dogan T, Doppelt-Azeroual O, Emery L, Gasteiger E, Gatter T, Goldberg T, Grosjean M, Grüning B, Helmer-Citterich M, Ienasescu H, Ioannidis V, Jespersen MC, Jimenez R, Juty N, Juvan P, Koch M, Laibe C, Li JW, Licata L, Mareuil F, Mičetić I, Friborg RM, Moretti S, Morris C, Möller S, Nenadic A, Peterson H, Profiti G, Rice P, Romano P, Roncaglia P, Saidi R, Schafferhans A, Schwämmle V, Smith C, Sperotto MM, Stockinger H, Vařeková RS, Tosatto SC, de la Torre V, Uva P, Via A, Yachdav G, Zambelli F, Vriend G, Rost B, Parkinson H, Løngreen P, Brunak S. Ison J, et al. Among authors: berka k. Nucleic Acids Res. 2016 Jan 4;44(D1):D38-47. doi: 10.1093/nar/gkv1116. Epub 2015 Nov 3. Nucleic Acids Res. 2016. PMID: 26538599 Free PMC article.
ChannelsDB: database of biomacromolecular tunnels and pores.
Pravda L, Sehnal D, Svobodová Vareková R, Navrátilová V, Toušek D, Berka K, Otyepka M, Koca J. Pravda L, et al. Among authors: berka k. Nucleic Acids Res. 2018 Jan 4;46(D1):D399-D405. doi: 10.1093/nar/gkx868. Nucleic Acids Res. 2018. PMID: 29036719 Free PMC article.
Automated Family-Wide Annotation of Secondary Structure Elements.
Midlik A, Hutařová Vařeková I, Hutař J, Moturu TR, Navrátilová V, Koča J, Berka K, Svobodová Vařeková R. Midlik A, et al. Among authors: berka k. Methods Mol Biol. 2019;1958:47-71. doi: 10.1007/978-1-4939-9161-7_3. Methods Mol Biol. 2019. PMID: 30945213
95 results