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1

Machine Learning in Enzyme Engineering

Mazurenko, Stanislav, Prokop, Zbyněk, Damborský, Jiří

Journal:

Year:

2019

File:

PDF, 891 KB

2019

2

The use of a microbial contact toxicity test for evaluating cadmium bioavailability in soil

Zbyněk Prokop, Ivan Holoubek

Journal:

Journal of Soils and Sediments

Year:

2001

Language:

english

File:

PDF, 728 KB

english, 2001

3

Interfacing Microwells with Nanoliter Compartments: A Sampler Generating High-Resolution Concentration Gradients for Quantitative Biochemical Analyses in Droplets

Gielen, Fabrice, Buryska, Tomas, Vliet, Liisa Van, Butz, Maren, Damborsky, Jiri, Prokop, Zbynek, Hollfelder, Florian

Journal:

Analytical Chemistry

Year:

2015

Language:

english

File:

PDF, 3.12 MB

english, 2015

4

Conformational Changes Allow Processing of Bulky Substrates by a Haloalkane Dehalogenase with a Small and Buried Active Site

Kokkonen, Piia, Bednar, David, Dockalova, Veronika, Prokop, Zbynek, Damborsky, Jiri

Journal:

Journal of Biological Chemistry

Year:

2018

Language:

english

File:

PDF, 830 KB

english, 2018

5

Controlled oil/water partitioning of hydrophobic substrates extends the bioanalytical applications of droplet-based microfluidics

Buryska, Tomas, Vasina, Michal, Gielen, Fabrice, Vanacek, Pavel, van Vliet, Liisa, Jezek, Jan, Pilat, Zdenek, Zemanek, Pavel, Damborský, Jiří, Hollfelder, Florian, Prokop, Zbyněk

Journal:

Analytical Chemistry

Year:

2019

Language:

english

File:

PDF, 592 KB

english, 2019

6

Enantioselectivity of Haloalkane Dehalogenases and its Modulation by Surface Loop Engineering

Zbynek Prokop, Yukari Sato, Jan Brezovsky, Tomas Mozga, Radka Chaloupkova, Tana Koudelakova, Petr Jerabek, Veronika Stepankova, Ryo Natsume, Jan G. E. van Leeuwen, Dick B. Janssen, Jan Florian, Yuji N

Journal:

Angewandte Chemie

Year:

2010

Language:

english

File:

PDF, 658 KB

english, 2010

7

Enantioselectivity of Haloalkane Dehalogenases and its Modulation by Surface Loop Engineering

Zbynek Prokop, Yukari Sato, Jan Brezovsky, Tomas Mozga, Radka Chaloupkova, Tana Koudelakova, Petr Jerabek, Veronika Stepankova, Ryo Natsume, Jan G. E. van Leeuwen, Dick B. Janssen, Jan Florian, Yuji N

Journal:

Angewandte Chemie International Edition

Year:

2010

Language:

english

File:

PDF, 694 KB

english, 2010

8

ChemInform Abstract: Chiral Aliphatic Hydroxy Compounds in Nature: A Review of Biological Functions and Practical Applications

Tomas Mozga, Zbynek Prokop, Radka Chaloupkova, Jiri Damborsky

Journal:

Year:

2010

File:

PDF, 15 KB

2010

9

Degradation of β-hexachlorocyclohexane by haloalkane dehalogenase LinB from γ-hexachlorocyclohexane-utilizing bacteriumSphingobiumsp. MI1205

Michihiro Ito, Zbyňek Prokop, Martin Klvaňa, Yoshiyuki Otsubo, Masataka Tsuda, Jiří Damborský, Yuji Nagata

Journal:

Archives of Microbiology

Year:

2007

Language:

english

File:

PDF, 707 KB

english, 2007

10

Development of an enzymatic fiber-optic biosensor for detection of halogenated hydrocarbons

Sarka Bidmanova, Radka Chaloupkova, Jiri Damborsky, Zbynek Prokop

Journal:

Analytical and Bioanalytical Chemistry

Year:

2010

Language:

english

File:

PDF, 223 KB

english, 2010

11

Stereoselectivity and conformational stability of haloalkane dehalogenase DbjA from Bradyrhizobium japonicum USDA110: the effect of pH and temperature

Radka Chaloupkova, Zbynek Prokop, Yukari Sato, Yuji Nagata, Jiri Damborsky

Journal:

Year:

2011

Language:

english

File:

PDF, 411 KB

english, 2011

12

Redesigning dehalogenase access tunnels as a strategy for degrading an anthropogenic substrate

Pavlova, Martina, Klvana, Martin, Prokop, Zbynek, Chaloupkova, Radka, Banas, Pavel, Otyepka, Michal, Wade, Rebecca C, Tsuda, Masataka, Nagata, Yuji, Damborsky, Jiri

Journal:

Nature Chemical Biology

Year:

2009

Language:

english

File:

PDF, 561 KB

english, 2009

13

Enzymatic Reaction Coupled with Flow-Injection Analysis with Charged Aerosol, Coulometric, or Amperometric Detection for Estimation of Contamination of the Environment by Pesticides

Radka Mikelova, Zbynek Prokop, Karel Stejskal, Vojtech Adam, Miroslava Beklova, Libuse Trnkova, Bohumila Kulichova, Ales Horna, Radka Chaloupkova, Jiri Damborsky, Rene Kizek

Journal:

Chromatographia

Year:

2008

Language:

english

File:

PDF, 427 KB

english, 2008

14

Enzymes fight chemical weapons

Zbyněk Prokop, Frantisěk Opluštil, Joseph DeFrank, Jiří Damborský

Journal:

Biotechnology Journal

Year:

2006

Language:

english

File:

PDF, 677 KB

english, 2006

15

Perspectives: Biotechnology in Czech Republic, the past and the future

Jirí Damborský, Zbyněk Prokop, Michal Kostka

Journal:

Biotechnology Journal

Year:

2006

Language:

english

File:

PDF, 525 KB

english, 2006

16

Conjugation of 5(6)-carboxyfluorescein and 5(6)-carboxynaphthofluorescein with bovine serum albumin and their immobilization for optical pH sensing

Sarka Bidmanova, Antonin Hlavacek, Jiri Damborsky, Zbynek Prokop

Journal:

Sensors and Actuators B: Chemical

Year:

2012

Language:

english

File:

PDF, 601 KB

english, 2012

17

Haloalkane dehalogenases: Biotechnological applications

Tana Koudelakova, Sarka Bidmanova, Pavel Dvorak, Antonin Pavelka, Radka Chaloupkova, Zbynek Prokop, Prof. Jiri Damborsky

Journal:

Biotechnology Journal

Year:

2012

Language:

english

File:

PDF, 1.08 MB

english, 2012

18

Quantitative structure–activity relationships for toxicity and genotoxicity of halogenated aliphatic compounds: Wing spot test of Drosophila melanogaster

Karel Chroust, Martina Pavlová, Zbyněk Prokop, Jan Mendel, Kateřina Božková, Zdeněk Kubát, Veronika Zajı´čková, Jiřı´ Damborský

Journal:

Year:

2007

Language:

english

File:

PDF, 159 KB

english, 2007

19

Pathways and Mechanisms for Product Release in the Engineered Haloalkane Dehalogenases Explored Using Classical and Random Acceleration Molecular Dynamics Simulations

Martin Klvana, Martina Pavlova, Tana Koudelakova, Radka Chaloupkova, Pavel Dvorak, Zbynek Prokop, Alena Stsiapanava, Michal Kuty, Ivana Kuta-Smatanova, Jan Dohnalek, Petr Kulhanek, Rebecca C. Wade, Ji

Journal:

Journal of Molecular Biology

Year:

2009

Language:

english

File:

PDF, 678 KB

english, 2009

20

The identification of catalytic pentad in the haloalkane dehalogenase DhmA from Mycobacterium avium N85: Reaction mechanism and molecular evolution

Martina Pavlová, Martin Klvaňa, Andrea Jesenská, Zbyněk Prokop, Hana Konečná, Takashi Sato, Masataka Tsuda, Yuji Nagata, Jiří Damborský

Journal:

Journal of Structural Biology

Year:

2007

Language:

english

File:

PDF, 793 KB

english, 2007

21

Development of a microtiter plate-based method for determination of degradation profile of nitrophenolic compounds

Ludmila Tvrzová, Zbyněk Prokop, Jitka Navrátilová, Radka Müllerová, Jiří Neča

Journal:

Journal of Microbiological Methods

Year:

2006

Language:

english

File:

PDF, 129 KB

english, 2006

22

Expression of glycosylated haloalkane dehalogenase LinB in Pichia pastoris

Takashi Nakamura, Marcel Zámocký, Zbyněk Zdráhal, Radka Chaloupková, Marta Monincová, Zbyněk Prokop, Yuji Nagata, Jiří Damborský

Journal:

Protein Expression and Purification

Year:

2006

Language:

english

File:

PDF, 507 KB

english, 2006

23

Halide-Stabilizing Residues of Haloalkane Dehalogenases Studied by Quantum Mechanic Calculations and Site-Directed Mutagenesis †

Boháč, Michal, Nagata, Yuji, Prokop, Zbyněk, Prokop, Martin, Monincová, Marta, Tsuda, Masataka, Koča, Jaroslav, Damborský, Jiří

Journal:

Year:

2002

Language:

english

File:

PDF, 282 KB

english, 2002

24

Expansion of Access Tunnels and Active-Site Cavities Influence Activity of Haloalkane Dehalogenases in Organic Cosolvents

Stepankova, Veronika, Khabiri, Morteza, Brezovsky, Jan, Pavelka, Antonin, Sykora, Jan, Amaro, Mariana, Minofar, Babak, Prokop, Zbynek, Hof, Martin, Ettrich, Rudiger, Chaloupkova, Radka, Damborsky, Jir

Journal:

Year:

2013

Language:

english

File:

PDF, 742 KB

english, 2013

25

Chiral aliphatic hydroxy compounds in nature: A review of biological functions and practical applications

Mozga, Tomáš, Prokop, Zbyněk, Chaloupková, Radka, Damborský, Jiří

Journal:

Collection of Czechoslovak Chemical Communications

Year:

2009

Language:

english

File:

PDF, 505 KB

english, 2009

26

The effect of a unique halide-stabilizing residue on the catalytic properties of haloalkane dehalogenase DatA from Agrobacterium tumefaciens C58

Hasan, Khomaini, Gora, Artur, Brezovsky, Jan, Chaloupkova, Radka, Moskalikova, Hana, Fortova, Andrea, Nagata, Yuji, Damborsky, Jiri, Prokop, Zbynek

Journal:

Year:

2013

Language:

english

File:

PDF, 398 KB

english, 2013

27

Engineering Enzyme Stability and Resistance to an Organic Cosolvent by Modification of Residues in the Access Tunnel

Koudelakova, Tana, Chaloupkova, Radka, Brezovsky, Jan, Prokop, Zbynek, Sebestova, Eva, Hesseler, Martin, Khabiri, Morteza, Plevaka, Maryia, Kulik, Daryna, Kuta Smatanova, Ivana, Rezacova, Pavlina, Ett

Journal:

Angewandte Chemie International Edition

Year:

2013

Language:

english

File:

PDF, 1.27 MB

english, 2013

28

Strategies for Stabilization of Enzymes in Organic Solvents

Stepankova, Veronika, Bidmanova, Sarka, Koudelakova, Tana, Prokop, Zbynek, Chaloupkova, Radka, Damborsky, Jiri

Journal:

Year:

2013

Language:

english

File:

PDF, 1.17 MB

english, 2013

29

Dynamics and hydration explain failed functional transformation in dehalogenase design

Sykora, Jan, Brezovsky, Jan, Koudelakova, Tana, Lahoda, Maryna, Fortova, Andrea, Chernovets, Tatsiana, Chaloupkova, Radka, Stepankova, Veronika, Prokop, Zbynek, Smatanova, Ivana Kuta, Hof, Martin, Dam

Journal:

Nature Chemical Biology

Year:

2014

Language:

english

File:

PDF, 786 KB

english, 2014

30

Microscopic monitoring provides information on structure and properties during biocatalyst immobilization

Bidmanova, Sarka, Hrdlickova, Eva, Jaros, Josef, Ilkovics, Ladislav, Hampl, Ales, Damborsky, Jiri, Prokop, Zbynek

Journal:

Biotechnology Journal

Year:

2014

Language:

english

File:

PDF, 3.20 MB

english, 2014

31

Haloalkane Dehalogenase LinB from Sphingomonas paucimobilis UT26: X-ray Crystallographic Studies of Dehalogenation of Brominated Substrates †,‡

Streltsov, Victor A., Prokop, Zbyněk, Damborský, Jiří, Nagata, Yuji, Oakley, Aaron, Wilce, Matthew C. J.

Journal:

Year:

2003

Language:

english

File:

PDF, 575 KB

english, 2003

32

Release of Halide Ions from the Buried Active Site of the Haloalkane Dehalogenase LinB Revealed by Stopped-Flow Fluorescence Analysis and Free Energy Calculations

Hladilkova, Jana, Prokop, Zbynek, Chaloupkova, Radka, Damborsky, Jiri, Jungwirth, Pavel

Journal:

Journal of Physical Chemistry B

Year:

2013

Language:

english

File:

PDF, 2.24 MB

english, 2013

33

Exploring the Structure and Activity of Haloalkane Dehalogenase from Sphingomonas paucimobilis UT26: Evidence for Product- and Water-Mediated Inhibition †,‡

Oakley, Aaron J., Prokop, Zbyněk, Boháč, Michal, Kmuníček, Jan, Jedlička, Tomáš, Monincová, Marta, Kutá-Smatanová, Ivana, Nagata, Yuji, Damborský, Jiří, Wilce, Matthew C. J.

Journal:

Year:

2002

Language:

english

File:

PDF, 405 KB

english, 2002

34

[IEEE 2011 34th International Spring Seminar on Electronics Technology (ISSE) - Tratanska Lomnica, Slovakia (2011.05.11-2011.05.15)] Proceedings of the 2011 34th International Spring Seminar on Electronics Technology (ISSE) - Analyzer for fluorescent biosensing application

Sedlacek, Jiri, Bidmanova, Sarka, Prokop, Zbynek, Damborsky, Jiri, Mikel, Bretislav, Hubalek, Jaromir

Year:

2011

Language:

english

File:

PDF, 735 KB

english, 2011

35

Haloalkane Dehalogenase LinB from Sphingomonas paucimobilis UT26: X-ray Crystallographic Studies of Dehalogenation of Brominated Substrates

Streltsov, Victor A., Prokop, Zbyněk, Damborský, Jiří, Nagata, Yuji, Oakley, Aaron, Wilce, Matthew C. J.

Journal:

Year:

2003

Language:

english

File:

PDF, 56 KB

english, 2003

36

Immobilized Synthetic Pathway for Biodegradation of Toxic Recalcitrant Pollutant 1,2,3-Trichloropropane

Dvorak, Pavel, Bidmanova, Sarka, Damborsky, Jiri, Prokop, Zbynek

Journal:

Environmental Science & Technology

Year:

2014

Language:

english

File:

PDF, 1.81 MB

english, 2014

37

Computer-Assisted Engineering of the Synthetic Pathway for Biodegradation of a Toxic Persistent Pollutant

Kurumbang, Nagendra Prasad, Dvorak, Pavel, Bendl, Jaroslav, Brezovsky, Jan, Prokop, Zbynek, Damborsky, Jiri

Journal:

ACS Synthetic Biology

Year:

2014

Language:

english

File:

PDF, 1.72 MB

english, 2014

38

Maximizing the Efficiency of Multienzyme Process by Stoichiometry Optimization

Dvorak, Pavel, Kurumbang, Nagendra P., Bendl, Jaroslav, Brezovsky, Jan, Prokop, Zbynek, Damborsky, Jiri

Journal:

Year:

2014

Language:

english

File:

PDF, 1.11 MB

english, 2014

39

Mechanism-Based Discovery of Novel Substrates of Haloalkane Dehalogenases Using in Silico Screening

Daniel, Lukas, Buryska, Tomas, Prokop, Zbynek, Damborsky, Jiri, Brezovsky, Jan

Journal:

Journal of Chemical Information and Modeling

Year:

2015

Language:

english

File:

PDF, 1.93 MB

english, 2015

40

Stepwise enhancement of catalytic performance of haloalkane dehalogenase LinB towards β-hexachlorocyclohexane

Moriuchi, Ryota, Tanaka, Hiroki, Nikawadori, Yuki, Ishitsuka, Mayuko, Ito, Michihiro, Ohtsubo, Yoshiyuki, Tsuda, Masataka, Damborsky, Jiri, Prokop, Zbynek, Nagata, Yuji

Journal:

Year:

2014

Language:

english

File:

PDF, 1.41 MB

english, 2014

41

Structural and functional analysis of a novel haloalkane dehalogenase with two halide-binding sites

Chaloupkova, Radka, Prudnikova, Tatyana, Rezacova, Pavlina, Prokop, Zbynek, Koudelakova, Tana, Daniel, Lukas, Brezovsky, Jan, Ikeda-Ohtsubo, Wakako, Sato, Yukari, Kuty, Michal, Nagata, Yuji, Kuta Smat

Journal:

Acta Crystallographica Section D Biological Crystallography

Year:

2014

Language:

english

File:

PDF, 1.40 MB

english, 2014

42

Parameters of Spike Trains Observed in a Short Time Window

Pawlas, Zbyněk, Klebanov, Lev B., Prokop, Martin, Lansky, Petr

Journal:

Neural Computation

Year:

2008

Language:

english

File:

PDF, 231 KB

english, 2008

43

Exacerbation of substrate toxicity by IPTG inEscherichia coliBL21(DE3) carrying a synthetic metabolic pathway

Dvorak, Pavel, Chrast, Lukas, Nikel, Pablo I., Fedr, Radek, Soucek, Karel, Sedlackova, Miroslava, Chaloupkova, Radka, de Lorenzo, Víctor, Prokop, Zbynek, Damborsky, Jiri

Journal:

Microbial Cell Factories

Year:

2015

Language:

english

File:

PDF, 2.37 MB

english, 2015

44

Bioavailability and mobility of organic contaminants in soil: new three-step ecotoxicological evaluation

Prokop, Zbyněk, Nečasová, Anežka, Klánová, Jana, Čupr, Pavel

Journal:

Environmental Science and Pollution Research

Year:

2016

Language:

english

File:

PDF, 746 KB

english, 2016

45

Enzyme based test stripes for the visual or photographic detection and quantitation of gaseous sulfur mustard

Bidmanova, Sarka, Steiner, Mark Steven, Stepan, Martin, Vymazalova, Kamila, Gruber, Michael Andreas, Duerkop, Axel, Damborsky, Jiri, Prokop, Zbynek, Wolfbeis, Otto S.

Journal:

Analytical Chemistry

Year:

2016

Language:

english

File:

PDF, 572 KB

english, 2016

46

Regio- and Enantioselective Sequential Dehalogenation of rac-1,3-Dibromobutane by Haloalkane Dehalogenase LinB

Gross, Johannes, Prokop, Zbyněk, Janssen, Dick, Faber, Kurt, Hall, Mélanie

Journal:

Year:

2016

Language:

english

File:

PDF, 609 KB

english, 2016

47

The dynamics of xylem sap pH under drought: a universal response in herbs?

Gloser, Vít, Korovetska, Halyna, Martín-Vertedor, Ana Isabel, Hájíčková, Martina, Prokop, Zbyněk, Wilkinson, Sally, Davies, William

Journal:

Year:

2016

Language:

english

File:

PDF, 1.23 MB

english, 2016

48

Engineering Enzyme Stability and Resistance to an Organic Cosolvent by Modification of Residues in the Access Tunnel

Koudelakova, Tana, Chaloupkova, Radka, Brezovsky, Jan, Prokop, Zbynek, Sebestova, Eva, Hesseler, Martin, Khabiri, Morteza, Plevaka, Maryia, Kulik, Daryna, Kuta Smatanova, Ivana, Rezacova, Pavlina, Ett

Journal:

Angewandte Chemie

Year:

2013

Language:

english

File:

PDF, 1.23 MB

english, 2013

49

Engineering a de novo transport tunnel

Brezovsky, Jan, Babkova, Petra, Degtjarik, Oksana, Fortova, Andrea, Gora, Artur, Iermak, Iuliia, Rezacova, Pavlina, Dvorak, Pavel, Kuta Smatanova, Ivana, Prokop, Zbynek, Chaloupkova, Radka, Damborsky,

Journal:

Year:

2016

Language:

english

File:

PDF, 1.47 MB

english, 2016

50

Kinetics of binding of fluorescent ligands to enzymes with engineered access tunnels

Kaushik, Shubhangi, Prokop, Zbynek, Damborsky, Jiri, Chaloupkova, Radka

Journal:

Year:

2016

Language:

english

File:

PDF, 954 KB

english, 2016

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