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1

Stepwise dissection and visualization of the catalytic mechanism of haloalkane dehalogenase LinB using molecular dynamics simulations and computer graphics

Ana Negri, Esther Marco, Jiri Damborsky, Federico Gago

Journal:

Journal of Molecular Graphics and Modelling

Year:

2007

Language:

english

File:

PDF, 1.20 MB

english, 2007

2

Machine Learning in Enzyme Engineering

Mazurenko, Stanislav, Prokop, Zbyněk, Damborský, Jiří

Journal:

Year:

2019

File:

PDF, 891 KB

2019

3

Computational tools for designing and engineering enzymes

Damborsky, Jiri, Brezovsky, Jan

Journal:

Current Opinion in Chemical Biology

Year:

2014

Language:

english

File:

PDF, 1.49 MB

english, 2014

4

Comparison of catalysis by haloalkane dehalogenases in aqueous solutions of deep eutectic and organic solvents

Stepankova, Veronika, Vanacek, Pavel, Damborsky, Jiri, Chaloupkova, Radka

Journal:

Green Chemistry

Year:

2014

Language:

english

File:

PDF, 882 KB

english, 2014

5

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

6

Analysis of the DNA-binding activity of p53 mutants using functional protein microarrays and its relationship to transcriptional activation

Malcikova, Jitka, Tichy, Boris, Damborsky, Jiri, Kabathova, Jitka, Trbusek, Martin, Mayer, Jiri, Pospisilova, Sarka

Journal:

Biological Chemistry

Year:

2010

Language:

english

File:

PDF, 339 KB

english, 2010

7

HotSpot Wizard 2.0: automated design of site-specific mutations and smart libraries in protein engineering

Bendl, Jaroslav, Stourac, Jan, Sebestova, Eva, Vavra, Ondrej, Musil, Milos, Brezovsky, Jan, Damborsky, Jiri

Journal:

Nucleic Acids Research

Year:

2016

Language:

english

File:

PDF, 2.37 MB

english, 2016

8

Bioremediation 3 . 0 : Engineering pollutant-removing bacteria in the times of systemic biology

Dvořák, Pavel, Nikel, Pablo I., Damborský, Jiří, de Lorenzo, Víctor

Journal:

Biotechnology Advances

Year:

2017

Language:

english

File:

PDF, 2.23 MB

english, 2017

9

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

10

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

11

Mechanism-based Quantitative Structure–Biodegradability Relationships for Hydrolytic Dehalogenation of Chloro- and Bromo-Alkenes

Jiří Damborský, Anders Berglund, Michal Kutý, Alena Ansorgová, Yuji Nagata, Michael Sjöström

Journal:

Molecular Informatics

Year:

1998

Language:

english

File:

PDF, 257 KB

english, 1998

12

Impact of Orthogonal Signal Correction (OSC) on the Predictive Ability of CoMFA Models for the Ciliate Toxicity of Nitrobenzenes

Michal Boháč, Björn Loeprecht, Jiří Damborský, Gerrit Schüürmann

Journal:

Molecular Informatics

Year:

2002

Language:

english

File:

PDF, 646 KB

english, 2002

13

Plectin repeats and modules: strategic cysteines and their presumed impact on cytolinker functions

Lubomír Janda, Jiří Damborský, Günther A. Rezniczek, Gerhard Wiche

Journal:

Year:

2001

Language:

english

File:

PDF, 234 KB

english, 2001

14

Binding of Fatty Acids to β-Cryptogein: Quantitative Structure—Activity Relationships and Design of Selective Protein Mutants.

Petr Dobes, Jan Kmunicek, Vladimir Mikes, Jiri Damborsky

Journal:

Year:

2005

File:

PDF, 9 KB

2005

15

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

16

Molecular orbital calculations to describe microbial reductive dechlorination of polychlorinated dioxins

Mary M. Lynam, Michal Kuty, Jiri Damborsky, Jaroslav Koca, Peter Adriaens

Journal:

Environmental Toxicology and Chemistry

Year:

1998

Language:

english

File:

PDF, 144 KB

english, 1998

17

Structure–specificity relationships for haloalkane dehalogenases

Jiří Damborský, Emiel Rorije, Andrea Jesenská, Yuji Nagata, Gilles Klopman, Willie J. G. M. Peijnenburg

Journal:

Environmental Toxicology and Chemistry

Year:

2001

Language:

english

File:

PDF, 77 KB

english, 2001

18

Novel germline BRCA1 and BRCA2 mutations in breast and breast/ovarian cancer families from the Czech Republic

Eva Machackova, Jiri Damborsky, Dalibor Valik, Lenka Foretova

Journal:

Year:

2001

Language:

english

File:

PDF, 70 KB

english, 2001

19

Computational tools for designing and engineering biocatalysts

Jiri Damborsky, Jan Brezovsky

Journal:

Current Opinion in Chemical Biology

Year:

2009

Language:

english

File:

PDF, 1.13 MB

english, 2009

20

Systems biology at work

Vítor A.P. Martins dos Santos, Jiri Damborsky

Journal:

Current Opinion in Biotechnology

Year:

2010

Language:

english

File:

PDF, 106 KB

english, 2010

21

Computer-assisted enzyme engineering by modification of tunnels, channels and gates

Artur Gora, Jan Brezovsky, Jiri Damborsky

Journal:

Current Opinion in Biotechnology

Year:

2011

Language:

english

File:

PDF, 93 KB

english, 2011

22

Elicitin–membrane interaction is driven by a positive charge on the protein surface: Role of Lys13 residue in lipids loading and resistance induction

Veronika Plešková, Tomáš Kašparovský, Michal Obořil, Nikola Ptáčková, Radka Chaloupková, Dokládal Ladislav, Jiří Damborský, Jan Lochman

Journal:

Plant Physiology and Biochemistry

Year:

2011

Language:

english

File:

PDF, 616 KB

english, 2011

23

Determination of haloalkane dehalogenase activity by capillary zone electrophoresis

Zdeněk Glatz, Mária V Marini, Michaela Wimmerová, Jiřı́ Damborský, Yuji Nagata

Journal:

Journal of Chromatography A

Year:

2000

Language:

english

File:

PDF, 139 KB

english, 2000

24

Retron reverse transcriptase rrtT is ubiquitous in strains of Salmonella enterica serovar Typhimurium

Jitka Matiasovicova, Marcela Faldynova, Martina Pravcova, Renata Karpiskova, Ivana Kolackova, Jiri Damborsky, Ivan Rychlik

Journal:

FEMS Microbiology Letters

Year:

2003

Language:

english

File:

PDF, 546 KB

english, 2003

25

High occurrence ofBRCA1intragenic rearrangements in hereditary breast and ovarian cancer syndrome in the Czech Republic

Petra Vasickova, Eva Machackova, Miroslava Lukesova, Jiri Damborsky, Ondrej Horky, Hana Pavlu, Jitka Kuklova, Veronika Kosinova, Marie Navratilova, Lenka Foretova

Journal:

BMC Medical Genetics

Year:

2007

Language:

english

File:

PDF, 1.23 MB

english, 2007

26

The new platinum-based anticancer agent LA-12 induces retinol binding protein 4in vivo

Pavel Bouchal, Jiri Jarkovsky, Kristyna Hrazdilova, Monika Dvorakova, Iva Struharova, Lenka Hernychova, Jiri Damborsky, Petr Sova, Borivoj Vojtesek

Journal:

Proteome Science

Year:

2011

Language:

english

File:

PDF, 455 KB

english, 2011

27

Identification of protein fold and catalytic residues of γ-hexachlorocyclohexane dehydrochlorinase LinA

Yuji Nagata, Katsuki Mori, Masamichi Takagi, Alexey G. Murzin, Jiří Damborský

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2001

Language:

english

File:

PDF, 181 KB

english, 2001

28

Phylogenetic analysis of haloalkane dehalogenases

Eva Chovancová, Jan Kosinski, Janusz M. Bujnicki, Jiří Damborský

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2007

Language:

english

File:

PDF, 937 KB

english, 2007

29

Second step of hydrolytic dehalogenation in haloalkane dehalogenase investigated by QM/MM methods

Michal Otyepka, Pavel Banáš, Alessandra Magistrato, Paolo Carloni, Jiří Damborský

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2008

Language:

english

File:

PDF, 354 KB

english, 2008

30

Role of SdiA inSalmonella entericaserovar Typhimurium physiology and virulence

Jiri Volf, Mojmir Sevcik, Hana Havlickova, Frantisek Sisak, Jiri Damborsky, Ivan Rychlik

Journal:

Archives of Microbiology

Year:

2002

Language:

english

File:

PDF, 97 KB

english, 2002

31

Identification ofSalmonella entericaserovar Typhimurium genes associated with growth suppression in stationary-phase nutrient broth cultures and in the chicken intestine

Ivan Rychlik, Gerald Martin, Ulrich Methner, Margaret Lovell, Lenka Cardova, Alena Sebkova, Mojmor Sevcik, Jiri Damborsky, Paul A. Barrow

Journal:

Archives of Microbiology

Year:

2002

Language:

english

File:

PDF, 712 KB

english, 2002

32

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

33

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

34

Mechanism of enhanced conversion of 1,2,3-trichloropropane by mutant haloalkane dehalogenase revealed by molecular modeling

Pavel Banáš, Michal Otyepka, Petr Jeřábek, Martin Petřek, Jiří Damborský

Journal:

Journal of Computer-Aided Molecular Design

Year:

2006

Language:

english

File:

PDF, 431 KB

english, 2006

35

Functional analysis of the aglycone-binding site of the maize β-glucosidase Zm-p60.1

Radka Dopitová, Pavel Mazura, Lubomír Janda, Radka Chaloupková, Petr Jeřábek, Jiří Damborský, Tomáš Filipi, Nagavalli S. Kiran, Břetislav Brzobohatý

Journal:

Year:

2008

Language:

english

File:

PDF, 727 KB

english, 2008

36

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

37

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

38

Sporulation as an effective strategy for the survival of bacteria in a biofilter with discontinuous operation

Jiří Damborský, Martina Damborská, Vlastimil Píštěk

Journal:

Biotechnology Letters

Year:

1999

Language:

english

File:

PDF, 44 KB

english, 1999

39

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

40

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

41

Identification of tunnels in proteins, nucleic acids, inorganic materials and molecular ensembles

Jiří Damborský, Martin Petřek, Pavel Banáš, Michal Otyepka

Journal:

Biotechnology Journal

Year:

2007

Language:

english

File:

PDF, 2.40 MB

english, 2007

42

Meeting Report: Protein design and evolution for biocatalysis August 30 – September 1, 2006, Greifswald, Germany

Journal:

Biotechnology Journal

Year:

2007

Language:

english

File:

PDF, 607 KB

english, 2007

43

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

44

Editorial: Protein design and engineering for biocatalysis

Journal:

Biotechnology Journal

Year:

2009

Language:

english

File:

PDF, 103 KB

english, 2009

45

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

46

TRITON: graphic software for rational engineering of enzymes

Jiřı́ Damborský, Martin Prokop, Jaroslav Koča

Journal:

Trends in Biochemical Sciences

Year:

2001

Language:

english

File:

PDF, 53 KB

english, 2001

47

CAVER: a new tool to explore routes from protein clefts, pockets and cavities

Martin Petřek, Michal Otyepka, Pavel Banáš, Pavlína Košinová, Jaroslav Koča, Jiří Damborský

Journal:

BMC Bioinformatics

Year:

2006

Language:

english

File:

PDF, 1.57 MB

english, 2006

48

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

49

Construction and Characterization of Histidine-Tagged Haloalkane Dehalogenase (LinB) of a New Substrate Class from a γ-Hexachlorocyclohexane-Degrading Bacterium, Sphingomonas paucimobilis UT26

Yuji Nagata, Kamila Hynková, Jiřı́ Damborský, Masamichi Takagi

Journal:

Protein Expression and Purification

Year:

1999

Language:

english

File:

PDF, 100 KB

english, 1999

50

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