Search Results - "Pavelka, Antonín"

MMTF-An efficient file format for the transmission, visualization, and analysis of macromolecular structures by Bradley, Anthony R, Rose, Alexander S, Pavelka, Antonín, Valasatava, Yana, Duarte, Jose M, Prlić, Andreas, Rose, Peter W

“…Recent advances in experimental techniques have led to a rapid growth in complexity, size, and number of macromolecular structures that are made available…”
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Recombinant production of human antimicrobial peptide LL- 37 and its secondary structure by Pavelka, Antonín, Vacek, Lukáš, Norek, Adam, Kobzová, Šárka, Janda, Lubomír

“…Antimicrobial peptides, including the human cathelicidin LL-37, offer a possible solution to the global problem of bacterial resistance to antibiotics. LL-37…”
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CAVER Analyst 2.0: analysis and visualization of channels and tunnels in protein structures and molecular dynamics trajectories by 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

“…Abstract Motivation Studying the transport paths of ligands, solvents, or ions in transmembrane proteins and proteins with buried binding sites is fundamental…”
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PredictSNP: robust and accurate consensus classifier for prediction of disease-related mutations by Bendl, Jaroslav, Stourac, Jan, Salanda, Ondrej, Pavelka, Antonin, Wieben, Eric D, Zendulka, Jaroslav, Brezovsky, Jan, Damborsky, Jiri

“…Single nucleotide variants represent a prevalent form of genetic variation. Mutations in the coding regions are frequently associated with the development of…”
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CAVER 3.0: a tool for the analysis of transport pathways in dynamic protein structures by 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

“…Tunnels and channels facilitate the transport of small molecules, ions and water solvent in a large variety of proteins. Characteristics of individual…”
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CAVER: Algorithms for Analyzing Dynamics of Tunnels in Macromolecules by Pavelka, Antonin, Sebestova, Eva, Kozlikova, Barbora, Brezovsky, Jan, Sochor, Jiri, Damborsky, Jiri

“…The biological function of a macromolecule often requires that a small molecule or ion is transported through its structure. The transport pathway often leads…”
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CAVER Analyst 1.0: graphic tool for interactive visualization and analysis of tunnels and channels in protein structures by 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

“…The transport of ligands, ions or solvent molecules into proteins with buried binding sites or through the membrane is enabled by protein tunnels and channels…”
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Haloalkane dehalogenases: Biotechnological applications by Koudelakova, Tana, Bidmanova, Sarka, Dvorak, Pavel, Pavelka, Antonin, Chaloupkova, Radka, Prokop, Zbynek, Damborsky, Jiri

“…Haloalkane dehalogenases (EC 3.8.1.5, HLDs) are α/β‐hydrolases which act to cleave carbon‐halogen bonds. Due to their unique catalytic mechanism, broad…”
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HotSpot Wizard: a web server for identification of hot spots in protein engineering by Pavelka, Antonin, Chovancova, Eva, Damborsky, Jiri

“…HotSpot Wizard is a web server for automatic identification of 'hot spots' for engineering of substrate specificity, activity or enantioselectivity of enzymes…”
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Software tools for identification, visualization and analysis of protein tunnels and channels by Brezovsky, Jan, Chovancova, Eva, Gora, Artur, Pavelka, Antonin, Biedermannova, Lada, Damborsky, Jiri

“…Protein structures contain highly complex systems of voids, making up specific features such as surface clefts or grooves, pockets, protrusions, cavities,…”
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Expansion of Access Tunnels and Active-Site Cavities Influence Activity of Haloalkane Dehalogenases in Organic Cosolvents by Stepankova, Veronika, Khabiri, Morteza, Brezovsky, Jan, Pavelka, Antonin, Sykora, Jan, Amaro, Mariana, Minofar, Babak, Prokop, Zbynek, Hof, Martin, Ettrich, Rudiger, Chaloupkova, Radka, Damborsky, Jiri

“…The use of enzymes for biocatalysis can be significantly enhanced by using organic cosolvents in the reaction mixtures. Selection of the cosolvent type and…”
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PredictSNP: Robust and Accurate Consensus Classifier for Prediction of Disease-Related Mutations: e1003440 by Bendl, Jaroslav, Stourac, Jan, Salanda, Ondrej, Pavelka, Antonin, Wieben, Eric D, Zendulka, Jaroslav, Brezovsky, Jan, Damborsky, Jiri

“…Single nucleotide variants represent a prevalent form of genetic variation. Mutations in the coding regions are frequently associated with the development of…”
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