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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: bednar d. Bioinformatics. 2014 Sep 15;30(18):2684-5. doi: 10.1093/bioinformatics/btu364. Epub 2014 May 29. Bioinformatics. 2014. PMID: 24876375
Site-specific analysis of protein hydration based on unnatural amino acid fluorescence.
Amaro M, Brezovský J, Kováčová S, Sýkora J, Bednář D, Němec V, Lišková V, Kurumbang NP, Beerens K, Chaloupková R, Paruch K, Hof M, Damborský J. Amaro M, et al. Among authors: bednar d. J Am Chem Soc. 2015 Apr 22;137(15):4988-92. doi: 10.1021/jacs.5b01681. Epub 2015 Apr 9. J Am Chem Soc. 2015. PMID: 25815779
FireProt: web server for automated design of thermostable proteins.
Musil M, Stourac J, Bendl J, Brezovsky J, Prokop Z, Zendulka J, Martinek T, Bednar D, Damborsky J. Musil M, et al. Among authors: bednar d. Nucleic Acids Res. 2017 Jul 3;45(W1):W393-W399. doi: 10.1093/nar/gkx285. Nucleic Acids Res. 2017. PMID: 28449074 Free PMC article.
Computer-assisted engineering of hyperstable fibroblast growth factor 2.
Dvorak P, Bednar D, Vanacek P, Balek L, Eiselleova L, Stepankova V, Sebestova E, Kunova Bosakova M, Konecna Z, Mazurenko S, Kunka A, Vanova T, Zoufalova K, Chaloupkova R, Brezovsky J, Krejci P, Prokop Z, Dvorak P, Damborsky J. Dvorak P, et al. Among authors: bednar d. Biotechnol Bioeng. 2018 Apr;115(4):850-862. doi: 10.1002/bit.26531. Epub 2018 Jan 24. Biotechnol Bioeng. 2018. PMID: 29278409
CAVER Analyst 2.0: analysis and visualization of channels and tunnels in protein structures and molecular dynamics trajectories.
Jurcik A, Bednar D, Byska J, Marques SM, Furmanova K, Daniel L, Kokkonen P, Brezovsky J, Strnad O, Stourac J, Pavelka A, Manak M, Damborsky J, Kozlikova B. Jurcik A, et al. Among authors: bednar d. Bioinformatics. 2018 Oct 15;34(20):3586-3588. doi: 10.1093/bioinformatics/bty386. Bioinformatics. 2018. PMID: 29741570 Free PMC article.
158 results