Jan Brezovsky
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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 Computational Biology 8 (10), e1002708, 2012
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
CAVER Analyst 2.0: analysis and visualization of channels and tunnels in protein structures and molecular dynamics trajectories
A Jurcik, D Bednar, J Byska, SM Marques, K Furmanova, L Daniel, ...
Bioinformatics 34 (20), 3586-3588, 2018
Gates of enzymes
A Gora, J Brezovsky, J Damborsky
Chemical reviews 113 (8), 5871-5923, 2013
Computational tools for designing and engineering enzymes
J Damborsky, J Brezovsky
Current opinion in chemical biology 19, 8-16, 2014
Caver Web 1.0: identification of tunnels and channels in proteins and analysis of ligand transport
J Stourac, O Vavra, P Kokkonen, J Filipovic, G Pinto, J Brezovsky, ...
Nucleic acids research 47 (W1), W414-W422, 2019
PredictSNP2: a unified platform for accurately evaluating SNP effects by exploiting the different characteristics of variants in distinct genomic regions
J Bendl, M Musil, J Štourač, J Zendulka, J Damborský*, J Brezovský*
PLoS computational biology 12 (5), e1004962, 2016
Tools and data services registry: a community effort to document bioinformatics resources
J Ison, K Rapacki, H Ménager, M Kalaš, E Rydza, P Chmura, C Anthon, ...
Nucleic acids research 44 (D1), D38-D47, 2016
FireProt: energy-and evolution-based computational design of thermostable multiple-point mutants
D Bednar, K Beerens, E Sebestova, J Bendl, S Khare, R Chaloupkova, ...
PLoS computational biology 11 (11), e1004556, 2015
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
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
Computational tools for designing and engineering biocatalysts
J Damborsky, J Brezovsky
Current opinion in chemical biology 13 (1), 26-34, 2009
FireProt: web server for automated design of thermostable proteins
M Musil, J Stourac, J Bendl, J Brezovsky, Z Prokop, J Zendulka, ...
Nucleic acids research 45 (W1), W393-W399, 2017
CAVER: algorithms for analyzing dynamics of tunnels in macromolecules
A Pavelka, E Sebestova, B Kozlikova, J Brezovsky, J Sochor, ...
IEEE/ACM transactions on computational biology and bioinformatics 13 (3 …, 2015
Substrate specificity of haloalkane dehalogenases
T Koudelakova, E Chovancova, J Brezovsky, M Monincova, A Fortova, ...
Biochemical Journal 435 (2), 345-354, 2011
Enantioselectivity of haloalkane dehalogenases and its modulation by surface loop engineering
Z Prokop*, Y Sato*, J Brezovsky*, T Mozga, R Chaloupkova, ...
Angewandte Chemie International Edition 49 (35), 6111-6115, 2010
Software tools for identification, visualization and analysis of protein tunnels and channels
J Brezovsky, E Chovancova, A Gora, A Pavelka, L Biedermannova, ...
Biotechnology advances 31 (1), 38-49, 2013
HotSpot Wizard 2.0: automated design of site-specific mutations and smart libraries in protein engineering
J Bendl, J Stourac, E Sebestova, O Vavra, M Musil, J Brezovsky*, ...
Nucleic acids research 44 (W1), W479-W487, 2016
Engineering a de novo transport tunnel
J Brezovsky*, P Babkova*, O Degtjarik, A Fortova, A Gora, I Iermak, ...
ACS Catalysis 6 (11), 7597-7610, 2016
Enzyme tunnels and gates as relevant targets in drug design
SM Marques, L Daniel, T Buryska, Z Prokop, J Brezovsky, J Damborsky
Medicinal Research Reviews 37 (5), 1095-1139, 2017
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