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Best matches for Jiří Damborský:

Bioremediation 3.0: Engineering pollutant-removing bacteria in the times of systemic biology. Dvořák P et al. Biotechnol Adv. (2017)

FireProt: web server for automated design of thermostable proteins. Musil M et al. Nucleic Acids Res. (2017)

Enzyme Tunnels and Gates As Relevant Targets in Drug Design. Marques SM et al. Med Res Rev. (2017)

Search results

Items: 1 to 20 of 142

1.

Caver Web 1.0: identification of tunnels and channels in proteins and analysis of ligand transport.

Stourac J, Vavra O, Kokkonen P, Filipovic J, Pinto G, Brezovsky J, Damborsky J, Bednar D.

Nucleic Acids Res. 2019 May 22. pii: gkz378. doi: 10.1093/nar/gkz378. [Epub ahead of print]

PMID:
31114897
2.

Crystal structure of the cold-adapted haloalkane dehalogenase DpcA from Psychrobacter cryohalolentis K5.

Tratsiak K, Prudnikova T, Drienovska I, Damborsky J, Brynda J, Pachl P, Kuty M, Chaloupkova R, Rezacova P, Kuta Smatanova I.

Acta Crystallogr F Struct Biol Commun. 2019 May 1;75(Pt 5):324-331. doi: 10.1107/S2053230X19002796. Epub 2019 Apr 24.

PMID:
31045561
3.

Engineering enzyme access tunnels.

Kokkonen P, Bednar D, Pinto G, Prokop Z, Damborsky J.

Biotechnol Adv. 2019 Apr 23. pii: S0734-9750(19)30067-9. doi: 10.1016/j.biotechadv.2019.04.008. [Epub ahead of print] Review.

PMID:
31026496
4.

CaverDock: A Novel Method for the Fast Analysis of Ligand Transport.

Filipovic J, Vavra O, Plhak J, Bednar D, Marques SM, Brezovsky J, Matyska L, Damborsky J.

IEEE/ACM Trans Comput Biol Bioinform. 2019 Mar 26. doi: 10.1109/TCBB.2019.2907492. [Epub ahead of print]

PMID:
30932844
5.

Computational Study of Protein-Ligand Unbinding for Enzyme Engineering.

Marques SM, Bednar D, Damborsky J.

Front Chem. 2019 Jan 8;6:650. doi: 10.3389/fchem.2018.00650. eCollection 2018.

6.

Exploring the challenges of computational enzyme design by rebuilding the active site of a dehalogenase.

Jindal G, Slanska K, Kolev V, Damborsky J, Prokop Z, Warshel A.

Proc Natl Acad Sci U S A. 2019 Jan 8;116(2):389-394. doi: 10.1073/pnas.1804979115. Epub 2018 Dec 26.

PMID:
30587585
7.

Molecular Gating of an Engineered Enzyme Captured in Real Time.

Kokkonen P, Sykora J, Prokop Z, Ghose A, Bednar D, Amaro M, Beerens K, Bidmanova S, Slanska M, Brezovsky J, Damborsky J, Hof M.

J Am Chem Soc. 2018 Dec 26;140(51):17999-18008. doi: 10.1021/jacs.8b09848. Epub 2018 Dec 14.

PMID:
30501200
8.

Detection of Chloroalkanes by Surface-Enhanced Raman Spectroscopy in Microfluidic Chips.

Pilát Z, Kizovský M, Ježek J, Krátký S, Sobota J, Šiler M, Samek O, Buryška T, Vaňáček P, Damborský J, Prokop Z, Zemánek P.

Sensors (Basel). 2018 Sep 23;18(10). pii: E3212. doi: 10.3390/s18103212.

9.

Development of Fluorescent Assay for Monitoring of Dehalogenase Activity.

Nevolova S, Manaskova E, Mazurenko S, Damborsky J, Prokop Z.

Biotechnol J. 2019 Mar;14(3):e1800144. doi: 10.1002/biot.201800144. Epub 2018 Aug 28.

PMID:
30052322
10.

Sensitive operation of enzyme-based biodevices by advanced signal processing.

Mazurenko S, Bidmanova S, Kotlanova M, Damborsky J, Prokop Z.

PLoS One. 2018 Jun 18;13(6):e0198913. doi: 10.1371/journal.pone.0198913. eCollection 2018.

11.

Haloalkane Dehalogenases From Marine Organisms.

Kunka A, Damborsky J, Prokop Z.

Methods Enzymol. 2018;605:203-251. doi: 10.1016/bs.mie.2018.03.005. Epub 2018 May 28. Review.

PMID:
29909825
12.

Conformational changes allow processing of bulky substrates by a haloalkane dehalogenase with a small and buried active site.

Kokkonen P, Bednar D, Dockalova V, Prokop Z, Damborsky J.

J Biol Chem. 2018 Jul 20;293(29):11505-11512. doi: 10.1074/jbc.RA117.000328. Epub 2018 Jun 1.

PMID:
29858243
13.

HotSpot Wizard 3.0: web server for automated design of mutations and smart libraries based on sequence input information.

Sumbalova L, Stourac J, Martinek T, Bednar D, Damborsky J.

Nucleic Acids Res. 2018 Jul 2;46(W1):W356-W362. doi: 10.1093/nar/gky417.

14.

CalFitter: a web server for analysis of protein thermal denaturation data.

Mazurenko S, Stourac J, Kunka A, Nedeljkovic S, Bednar D, Prokop Z, Damborsky J.

Nucleic Acids Res. 2018 Jul 2;46(W1):W344-W349. doi: 10.1093/nar/gky358.

15.

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.

Bioinformatics. 2018 Oct 15;34(20):3586-3588. doi: 10.1093/bioinformatics/bty386.

16.

Impact of the access tunnel engineering on catalysis is strictly ligand-specific.

Kaushik S, Marques SM, Khirsariya P, Paruch K, Libichova L, Brezovsky J, Prokop Z, Chaloupkova R, Damborsky J.

FEBS J. 2018 Apr;285(8):1456-1476. doi: 10.1111/febs.14418. Epub 2018 Mar 25.

17.

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.

Biotechnol Bioeng. 2018 Apr;115(4):850-862. doi: 10.1002/bit.26531. Epub 2018 Jan 24.

PMID:
29278409
18.

Gram-scale production of recombinant microbial enzymes in shake flasks.

Chrast L, Chaloupkova R, Damborsky J.

FEMS Microbiol Lett. 2018 Feb 1;365(2). doi: 10.1093/femsle/fnx265.

PMID:
29228335
19.

Exploration of Protein Unfolding by Modelling Calorimetry Data from Reheating.

Mazurenko S, Kunka A, Beerens K, Johnson CM, Damborsky J, Prokop Z.

Sci Rep. 2017 Nov 24;7(1):16321. doi: 10.1038/s41598-017-16360-y.

20.

A Haloalkane Dehalogenase from a Marine Microbial Consortium Possessing Exceptionally Broad Substrate Specificity.

Buryska T, Babkova P, Vavra O, Damborsky J, Prokop Z.

Appl Environ Microbiol. 2018 Jan 2;84(2). pii: e01684-17. doi: 10.1128/AEM.01684-17. Print 2018 Jan 15.

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