CAVER Analyst 2.0: analysis and visualization of channels and tunnels in protein structures and molecular dynamics trajectories
Jurcik, Adam, Bednar, David, Byska, Jan, Marques, Sergio M, Furmanova, Katarina, Daniel, Lukas, Kokkonen, Piia, Brezovsky, Jan, Strnad, Ondrej, Stourac, Jan, Pavelka, Antonin, Manak, Martin, Damborsky, Jiri, Kozlikova, Barbora
Published in Bioinformatics (15.10.2018)
Published in Bioinformatics (15.10.2018)
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PredictSNP: robust and accurate consensus classifier for prediction of disease-related mutations
Bendl, Jaroslav, Stourac, Jan, Salanda, Ondrej, Pavelka, Antonin, Wieben, Eric D, Zendulka, Jaroslav, Brezovsky, Jan, Damborsky, Jiri
Published in PLoS computational biology (01.01.2014)
Published in PLoS computational biology (01.01.2014)
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CAVER 3.0: a tool for the analysis of transport pathways in dynamic protein structures
Chovancova, Eva, Pavelka, Antonin, Benes, Petr, Strnad, Ondrej, Brezovsky, Jan, Kozlikova, Barbora, Gora, Artur, Sustr, Vilem, Klvana, Martin, Medek, Petr, Biedermannova, Lada, Sochor, Jiri, Damborsky, Jiri
Published in PLoS computational biology (01.10.2012)
Published in PLoS computational biology (01.10.2012)
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FireProt: Energy- and Evolution-Based Computational Design of Thermostable Multiple-Point Mutants
Bednar, David, Beerens, Koen, Sebestova, Eva, Bendl, Jaroslav, Khare, Sagar, Chaloupkova, Radka, Prokop, Zbynek, Brezovsky, Jan, Baker, David, Damborsky, Jiri
Published in PLoS computational biology (01.11.2015)
Published in PLoS computational biology (01.11.2015)
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Journal Article
CAVER Analyst 1.0: graphic tool for interactive visualization and analysis of tunnels and channels in protein structures
Kozlikova, Barbora, Sebestova, Eva, Sustr, Vilem, Brezovsky, Jan, Strnad, Ondrej, Daniel, Lukas, Bednar, David, Pavelka, Antonin, Manak, Martin, Bezdeka, Martin, Benes, Petr, Kotry, Matus, Gora, Artur, Damborsky, Jiri, Sochor, Jiri
Published in Bioinformatics (Oxford, England) (15.09.2014)
Published in Bioinformatics (Oxford, England) (15.09.2014)
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Journal Article
Impact of the access tunnel engineering on catalysis is strictly ligand‐specific
Kaushik, Shubhangi, Marques, Sérgio M., Khirsariya, Prashant, Paruch, Kamil, Libichova, Lenka, Brezovsky, Jan, Prokop, Zbynek, Chaloupkova, Radka, Damborsky, Jiri
Published in The FEBS journal (01.04.2018)
Published in The FEBS journal (01.04.2018)
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Tools and data services registry: a community effort to document bioinformatics resources
Ison, Jon, Rapacki, Kristoffer, Ménager, Hervé, Kalaš, Matúš, Rydza, Emil, Chmura, Piotr, Anthon, Christian, Beard, Niall, Berka, Karel, Bolser, Dan, Booth, Tim, Bretaudeau, Anthony, Brezovsky, Jan, Casadio, Rita, Cesareni, Gianni, Coppens, Frederik, Cornell, Michael, Cuccuru, Gianmauro, Davidsen, Kristian, Vedova, Gianluca Della, Dogan, Tunca, Doppelt-Azeroual, Olivia, Emery, Laura, Gasteiger, Elisabeth, Gatter, Thomas, Goldberg, Tatyana, Grosjean, Marie, Grüning, Björn, Helmer-Citterich, Manuela, Ienasescu, Hans, Ioannidis, Vassilios, Jespersen, Martin Closter, Jimenez, Rafael, Juty, Nick, Juvan, Peter, Koch, Maximilian, Laibe, Camille, Li, Jing-Woei, Licata, Luana, Mareuil, Fabien, Mičetić, Ivan, Friborg, Rune Møllegaard, Moretti, Sebastien, Morris, Chris, Möller, Steffen, Nenadic, Aleksandra, Peterson, Hedi, Profiti, Giuseppe, Rice, Peter, Romano, Paolo, Roncaglia, Paola, Saidi, Rabie, Schafferhans, Andrea, Schwämmle, Veit, Smith, Callum, Sperotto, Maria Maddalena, Stockinger, Heinz, Vařeková, Radka Svobodová, Tosatto, Silvio C E, de la Torre, Victor, Uva, Paolo, Via, Allegra, Yachdav, Guy, Zambelli, Federico, Vriend, Gert, Rost, Burkhard, Parkinson, Helen, Løngreen, Peter, Brunak, Søren
Published in Nucleic acids research (04.01.2016)
Published in Nucleic acids research (04.01.2016)
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Computational Analysis of Protein Tunnels and Channels
Brezovsky, Jan, Kozlikova, Barbora, Damborsky, Jiri
Published in Methods in molecular biology (Clifton, N.J.) (2018)
Published in Methods in molecular biology (Clifton, N.J.) (2018)
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Journal Article
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, Ettrich, Rudiger, Bornscheuer, Uwe T., Damborsky, Jiri
Published in Angewandte Chemie (International ed.) (11.02.2013)
Published in Angewandte Chemie (International ed.) (11.02.2013)
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Substrate specificity of haloalkane dehalogenases
Koudelakova, Tana, Chovancova, Eva, Brezovsky, Jan, Monincova, Marta, Fortova, Andrea, Jarkovsky, Jiri, Damborsky, Jiri
Published in Biochemical journal (15.04.2011)
Published in Biochemical journal (15.04.2011)
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Divide-and-conquer approach to study protein tunnels in long molecular dynamics simulations
Sequeiros-Borja, Carlos, Surpeta, Bartlomiej, Marchlewski, Igor, Brezovsky, Jan
Published in MethodsX (01.01.2023)
Published in MethodsX (01.01.2023)
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Interaction of organic solvents with protein structures at protein-solvent interface
Khabiri, Morteza, Minofar, Babak, Brezovský, Jan, Damborský, Jiří, Ettrich, Rudiger
Published in Journal of molecular modeling (01.11.2013)
Published in Journal of molecular modeling (01.11.2013)
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Journal Article
Evolutionary Analysis As a Powerful Complement to Energy Calculations for Protein Stabilization
Beerens, Koen, Mazurenko, Stanislav, Kunka, Antonin, Marques, Sergio M, Hansen, Niels, Musil, Milos, Chaloupkova, Radka, Waterman, Jitka, Brezovsky, Jan, Bednar, David, Prokop, Zbynek, Damborsky, Jiri
Published in ACS catalysis (05.10.2018)
Published in ACS catalysis (05.10.2018)
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