Jiri Damborsky

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Jan BrezovskyLaboratory of Biomolecular Interactions and Transport, IIMCB in Warsaw and IBMIB, AMU in PoznanVerified email at iimcb.gov.pl
Jan ŠtouračMasaryk University, BrnoVerified email at mail.muni.cz
Antonín PavelkaMasaryk UniversityVerified email at fi.muni.cz
Barbora Kozlikovaassoc. prof., Masaryk UniversityVerified email at fi.muni.cz
Artur GóraBiotechnology Centre Silesian University of TechnologyVerified email at artgora.com
Dick B. JanssenUniversity of GroningenVerified email at rug.nl
Rebecca WadeHeidelberg Institute for Theoretical Studies and Heidelberg UniversityVerified email at h-its.org
Pavel DvořákAssistant Professor and PI at Masaryk University, Brno, Czech RepublicVerified email at sci.muni.cz
Jaroslav BendlIcahn School of Medicine at Mount Sinai, New YorkVerified email at fit.vutbr.cz
Pavlina RezacovaHead of Structural Biology, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech RepublicVerified email at uochb.cas.cz
Lukas DanielInstitute of Applied BiotechnologiesVerified email at mail.muni.cz
Jiri SochorProfessor of Computer Science, Masaryk UniversityVerified email at fi.muni.cz
Miloš MusilLoschmidt laboratoriesVerified email at stud.fit.vutbr.cz
Yukari SatoTohoku UniversityVerified email at ige.tohoku.ac.jp
Ondřej StrnadResearch Scientist at KAUSTVerified email at kaust.edu.sa
Stanislav MazurenkoPostdoc, Masaryk UniversityVerified email at mail.muni.cz
Rudi H. EttrichCollege of Biomedical Sciences, Larkin University, Miami, FL, USAVerified email at ularkin.org
Morteza KhabiriAssistant Professor of Biology, Quinnipiac UniversityVerified email at quinnipiac.edu
Lada BiedermannováResearch Associate, Institute of Biotechnology, Czech Academy of SciencesVerified email at ibt.cas.cz
Antonín KunkaMasarykova UniverzitaVerified email at mail.muni.cz

Jiri Damborsky

Masaryk University

Verified email at chemi.muni.cz - Homepage

Protein engineering Protein design


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CAVER 3.0: a tool for the analysis of transport pathways in dynamic protein structures E Chovancova, A Pavelka, P Benes, O Strnad, J Brezovsky, B Kozlikova, ... PLoS Comput Biol 8 (10), e1002708, 2012	769	2012
CAVER: a new tool to explore routes from protein clefts, pockets and cavities M Petřek, M Otyepka, P Banáš, P Košinová, J Koča, J Damborský BMC bioinformatics 7 (1), 1-9, 2006	565	2006
Strategies for stabilization of enzymes in organic solvents V Stepankova, S Bidmanova, T Koudelakova, Z Prokop, R Chaloupkova, ... Acs Catalysis 3 (12), 2823-2836, 2013	436	2013
PredictSNP: robust and accurate consensus classifier for prediction of disease-related mutations J Bendl, J Stourac, O Salanda, A Pavelka, ED Wieben, J Zendulka, ... PLoS Comput Biol 10 (1), e1003440, 2014	430	2014
Redesigning dehalogenase access tunnels as a strategy for degrading an anthropogenic substrate M Pavlova, M Klvana, Z Prokop, R Chaloupkova, P Banas, M Otyepka, ... Nature chemical biology 5 (10), 727-733, 2009	265	2009
HotSpot Wizard: a web server for identification of hot spots in protein engineering A Pavelka, E Chovancova, J Damborsky Nucleic acids research 37 (suppl_2), W376-W383, 2009	193	2009
Computational tools for designing and engineering enzymes J Damborsky, J Brezovsky Current opinion in chemical biology 19, 8-16, 2014	183	2014
Purification and characterization of a haloalkane dehalogenase of a new substrate class from a gamma-hexachlorocyclohexane-degrading bacterium, Sphingomonas paucimobilis UT26 Y Nagata, K Miyauchi, J Damborsky, K Manova, A Ansorgova, M Takagi Applied and Environmental Microbiology 63 (9), 3707-3710, 1997	179	1997
Crystal Structure of the Haloalkane Dehalogenase from Sphingomonas paucimobilis UT26^, J Marek, J Vévodová, IK Smatanová, Y Nagata, LA Svensson, J Newman, ... Biochemistry 39 (46), 14082-14086, 2000	177	2000
Biodegradation of 1, 2, 3-trichloropropane through directed evolution and heterologous expression of a haloalkane dehalogenase gene T Bosma, J Damborský, G Stucki, DB Janssen Applied and environmental microbiology 68 (7), 3582-3587, 2002	175	2002
Gates of enzymes A Gora, J Brezovsky, J Damborsky Chemical reviews 113 (8), 5871-5923, 2013	171	2013
Modification of activity and specificity of haloalkane dehalogenase from Sphingomonas paucimobilis UT26 by engineering of its entrance tunnel R Chaloupková, J Sýkorová, Z Prokop, A Jesenská, M Monincová, ... Journal of Biological Chemistry 278 (52), 52622-52628, 2003	171	2003
Haloalkane dehalogenases: biotechnological applications T Koudelakova, S Bidmanova, P Dvorak, A Pavelka, R Chaloupkova, ... Biotechnology journal 8 (1), 32-45, 2013	147	2013
CAVER Analyst 1.0: graphic tool for interactive visualization and analysis of tunnels and channels in protein structures B Kozlikova, E Sebestova, V Sustr, J Brezovsky, O Strnad, L Daniel, ... Bioinformatics 30 (18), 2684-2685, 2014	139	2014
Computational tools for designing and engineering biocatalysts J Damborsky, J Brezovsky Current opinion in chemical biology 13 (1), 26-34, 2009	135	2009
Bioremediation 3.0: engineering pollutant-removing bacteria in the times of systemic biology P Dvořák, PI Nikel, J Damborský, V de Lorenzo Biotechnology advances 35 (7), 845-866, 2017	130	2017
Phylogenetic analysis of haloalkane dehalogenases E Chovancová, J Kosinski, JM Bujnicki, J Damborský PROTEINS: Structure, Function, and Bioinformatics 67 (2), 305-316, 2007	128	2007
Engineering enzyme stability and resistance to an organic cosolvent by modification of residues in the access tunnel T Koudelakova, R Chaloupkova, J Brezovsky, Z Prokop, E Sebestova, ... Angewandte Chemie 125 (7), 2013-2017, 2013	126	2013
Enantioselectivity of haloalkane dehalogenases and its modulation by surface loop engineering Z Prokop, Y Sato, J Brezovsky, T Mozga, R Chaloupkova, T Koudelakova, ... Angewandte Chemie International Edition 49 (35), 6111-6115, 2010	123	2010
Substrate specificity of haloalkane dehalogenases T Koudelakova, E Chovancova, J Brezovsky, M Monincova, A Fortova, ... Biochemical Journal 435 (2), 345-354, 2011	116	2011

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