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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: brezovsky j. 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.
CAVER 3.0: a tool for the analysis of transport pathways in dynamic protein structures.
Chovancova E, Pavelka A, Benes P, Strnad O, Brezovsky J, Kozlikova B, Gora A, Sustr V, Klvana M, Medek P, Biedermannova L, Sochor J, Damborsky J. Chovancova E, et al. Among authors: brezovsky j. PLoS Comput Biol. 2012;8(10):e1002708. doi: 10.1371/journal.pcbi.1002708. Epub 2012 Oct 18. PLoS Comput Biol. 2012. PMID: 23093919 Free PMC article.
Computational tools for designing and engineering enzymes.
Damborsky J, Brezovsky J. Damborsky J, et al. Among authors: brezovsky j. Curr Opin Chem Biol. 2014 Apr;19:8-16. doi: 10.1016/j.cbpa.2013.12.003. Epub 2013 Dec 31. Curr Opin Chem Biol. 2014. PMID: 24780274 Review.
CAVER Analyst 1.0: graphic tool for interactive visualization and analysis of tunnels and channels in protein structures.
Kozlikova B, Sebestova E, Sustr V, Brezovsky J, Strnad O, Daniel L, Bednar D, Pavelka A, Manak M, Bezdeka M, Benes P, Kotry M, Gora A, Damborsky J, Sochor J. Kozlikova B, et al. Among authors: brezovsky j. Bioinformatics. 2014 Sep 15;30(18):2684-5. doi: 10.1093/bioinformatics/btu364. Epub 2014 May 29. Bioinformatics. 2014. PMID: 24876375
Computational tools for designing smart libraries.
Sebestova E, Bendl J, Brezovsky J, Damborsky J. Sebestova E, et al. Among authors: brezovsky j. Methods Mol Biol. 2014;1179:291-314. doi: 10.1007/978-1-4939-1053-3_20. Methods Mol Biol. 2014. PMID: 25055786
52 results