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Haloalkane dehalogenases: Biotechnological applications

Tana Koudelakova, Sarka Bidmanova, Pavel Dvorak, Antonin Pavelka, Radka Chaloupkova, Zbynek Prokop, Jiri Damborsky
2012 Biotechnology Journal  
Pavelka 1 , Radka Chaloupkova 1 , Zbynek Prokop 1,2 and Jiri Damborsky 1,2 Expression The expression of HLDs in their natural hosts was studied with DhaA, DhlA and LinB, which were isolated from bacterial  ...  important for various practical applications, such as expression, substrate Review Haloalkane dehalogenases: Biotechnological applications * Tana Koudelakova 1 , Sarka Bidmanova 1 , Pavel Dvorak 1 , Antonin  ... 
doi:10.1002/biot.201100486 pmid:22965918 fatcat:vfjjlsl2ljeo7lbealbp5ccwda

Software tools for identification, visualization and analysis of protein tunnels and channels

Jan Brezovsky, Eva Chovancova, Artur Gora, Antonin Pavelka, Lada Biedermannova, Jiri Damborsky
2013 Biotechnology Advances  
doi:10.1016/j.biotechadv.2012.02.002 pmid:22349130 fatcat:qm6uw2qdfvbcbms4niik5tbqnu

MMTF - an efficient file format for the transmission, visualization, and analysis of macromolecular structures [article]

Anthony R Bradley, Alexander S Rose, Antonin Pavelka, Yana Valasatava, Jose M Duarte, Andreas Prlic, Peter W Rose
2017 bioRxiv   pre-print
Recent advances in experimental techniques have led to a rapid growth in complexity, size, and number of macromolecular structures that are made available through the Protein Data Bank. This creates a challenge for macromolecular visualization and analysis. Macromolecular structure files, such as PDB or PDBx/mmCIF files can be slow to transfer, parse, and hard to incorporate into third-party software tools. Here, we present a new binary and compressed data representation, the MacroMolecular
more » ... smission Format, MMTF, as well as software implementations in several languages that have been developed around it, which address these issues. We describe the new format and its APIs and demonstrate that it is several times faster to parse, and about a quarter of the file size of the current standard format, PDBx/mmCIF. As a consequence of the new data representation, it is now possible to visualize structures with millions of atoms in a web browser, keep the whole PDB archive in memory or parse it within few minutes on average computers, which opens up a new way of thinking how to implement efficient algorithms in structural bioinformatics. The PDB archive is available in MMTF file format through web services and data are updated on a weekly basis.
doi:10.1101/122689 fatcat:xht33wu2rrddlckxx5vav7izv4

PredictSNP: Robust and Accurate Consensus Classifier for Prediction of Disease-Related Mutations

Jaroslav Bendl, Jan Stourac, Ondrej Salanda, Antonin Pavelka, Eric D. Wieben, Jaroslav Zendulka, Jan Brezovsky, Jiri Damborsky, Paul P. Gardner
2014 PLoS Computational Biology  
Single nucleotide variants represent a prevalent form of genetic variation. Mutations in the coding regions are frequently associated with the development of various genetic diseases. Computational tools for the prediction of the effects of mutations on protein function are very important for analysis of single nucleotide variants and their prioritization for experimental characterization. Many computational tools are already widely employed for this purpose. Unfortunately, their comparison and
more » ... further improvement is hindered by large overlaps between the training datasets and benchmark datasets, which lead to biased and overly optimistic reported performances. In this study, we have constructed three independent datasets by removing all duplicities, inconsistencies and mutations previously used in the training of evaluated tools. The benchmark dataset containing over 43,000 mutations was employed for the unbiased evaluation of eight established prediction tools: MAPP, nsSNPAnalyzer, PANTHER, PhD-SNP, PolyPhen-1, PolyPhen-2, SIFT and SNAP. The six best performing tools were combined into a consensus classifier PredictSNP, resulting into significantly improved prediction performance, and at the same time returned results for all mutations, confirming that consensus prediction represents an accurate and robust alternative to the predictions delivered by individual tools. A user-friendly web interface enables easy access to all eight prediction tools, the consensus classifier PredictSNP and annotations from the Protein Mutant Database and the UniProt database. The web server and the datasets are freely available to the academic community at
doi:10.1371/journal.pcbi.1003440 pmid:24453961 pmcid:PMC3894168 fatcat:5aldi7vjovcj3b5nv76frvt6gq

MMTF—An efficient file format for the transmission, visualization, and analysis of macromolecular structures

Anthony R. Bradley, Alexander S. Rose, Antonín Pavelka, Yana Valasatava, Jose M. Duarte, Andreas Prlić, Peter W. Rose, Dina Schneidman
2017 PLoS Computational Biology  
OPEN ACCESS Citation: Bradley AR, Rose AS, Pavelka A, Valasatava Y, Duarte JM, Prlić A, et al. (2017) MMTF-An efficient file format for the transmission, visualization, and analysis of macromolecular structures  ... 
doi:10.1371/journal.pcbi.1005575 pmid:28574982 pmcid:PMC5473584 fatcat:niriuttkdnhcdp2l5mfc6vocdq

CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures

Eva Chovancova, Antonin Pavelka, Petr Benes, Ondrej Strnad, Jan Brezovsky, Barbora Kozlikova, Artur Gora, Vilem Sustr, Martin Klvana, Petr Medek, Lada Biedermannova, Jiri Sochor (+2 others)
2012 PLoS Computational Biology  
Tunnels and channels facilitate the transport of small molecules, ions and water solvent in a large variety of proteins.
doi:10.1371/journal.pcbi.1002708 pmid:23093919 pmcid:PMC3475669 fatcat:3z5ldoikgbfg7paoo5abyrskji

CAVER Analyst 1.0: graphic tool for interactive visualization and analysis of tunnels and channels in protein structures

Barbora Kozlikova, Eva Sebestova, Vilem Sustr, Jan Brezovsky, Ondrej Strnad, Lukas Daniel, David Bednar, Antonin Pavelka, Martin Manak, Martin Bezdeka, Petr Benes, Matus Kotry (+3 others)
2014 Computer applications in the biosciences : CABIOS  
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. CAVER Analyst is a software tool for calculation, analysis and real-time visualization of access tunnels and channels in static and dynamic protein structures. It provides an intuitive graphic user interface for setting up the calculation and interactive exploration of identified tunnels/channels and their characteristics. Availability
more » ... d Implementation: CAVER Analyst is a multi-platform software written in JAVA. Binaries and documentation are freely available for non-commercial use at
doi:10.1093/bioinformatics/btu364 pmid:24876375 fatcat:ytbqgyu3mzf7bdztn256w6imqy

The Use of Environmental Methods for Studying the Fortification, Economic System and Natural Environment of a Hillfort from the Beginning of the Middle Bronze Age at Vrcovice, Czech Republic

Daniel Hlásek, Petra Houfková, Lenka Kováčiková, Antonín Majer, Jan Novák, Jaroslav Pavelka, Tomáš Bešta, Tereza Šálková
2014 Interdisciplinaria Archaeologica  
Pavelka, Vařeka 2008; John, Pavelka 2010 ).  ...  IANSA 2014 • V/1 • 31-47 Daniel Hlásek, Petra Houfková, Lenka Kovačiková, Antonín Majer, Jan Novák, Jaroslav Pavelka, Tomáš Bešta, Tereza Šálková: Anthracological analysis Charcoals of wood were found  ... 
doi:10.24916/iansa.2014.1.3 fatcat:j42ubqtjpzeedjrgr7ar4xmkb4

Czech Thomist Philosophers Write about Marxism (1945‒1948)
Čeští tomisté píší o marxismu (1945‒1948)

Petr Macek
2021 Studia theologica  
Antonín Čala, Dominik Pecka, Jaroslav Beneš and Miloslav Skácel.  ...  Možná nejjasněji ze všech zkoumaných textů vyjádřil rozdíl mezi oběma školami Artur Pavelka ve stati Křesťanský realismus, přírodní věda a dialektický materialismu.  ... 
doi:10.5507/sth.2020.043 fatcat:4is6hh47q5dd5d6iwop345gdkm

Page 627 of National Union Catalog Vol. 16, Issue [page]

1948 National Union Catalog  
Pavelka ausgear' “Bibliographie” : p. 39-:45 1. Paintings, Bohemian. 2. Paintings, Medieval. 3. Art, Gothic 1. Matéjfek, Antonin, ed. 1. Title. AC 40-1566 rev Vassar College. Library Prague.  ...  a tivodni stat’ napsal Antonin Matéjéek. 3. doplnéné a pfepracované vyd., Praha, Melantrich, 1950. P. '9 plates Mey col) Si cm. fy nd p. 31-36. ng Bohemia 2 moe — eyubouan. 1. Matéjtek, Antonin, ed.  ... 

Page 2644 of Mathematical Reviews Vol. , Issue 2001D [page]

2001 Mathematical Reviews  
Edited by Jan Pavelka, Gerard Tel and Miroslav BartoSek Lecture Notes in Computer Science, 1725. Springer-Verlag, Berlin, 1999. xiv+498 pp. $79.00.  ...  Lutz, Vikram Mhetre and Srid- har Srinivasan, Hard instances of hard problems (324-333); Petr Janéar, Antonin Kuéera and Faron Moller, Simulation and bisim- ulation over one-counter processes (334-345)  ... 

ICCC 2020 Breaker Page

2020 2020 21th International Carpathian Control Conference (ICCC)  
Andrzej Jozef Trojan Ján Terpák Piotr Micek Ion Voinea Bogdan Sapiński Ewa Pawluszewicz Technical Papers The Inherent Velocity Limitation in Robust Robot Control Szilveszter Kovacs Marek Kliment Václav Pavelka  ...  Psychalinos Blas M Vinagre Tomas Skovranek Alexandra Fanca, Adela Puscasiu, Dan-Ioan Gota and Honoriu Valean Plenary Keynote Automatic Navigation System for 3D Robotic Laser Cladding Marcel Pástor Robert Palo Antonin  ... 
doi:10.1109/iccc49264.2020.9257253 fatcat:22ffqnxgnnbxbnv5iyby4td4ya

The Prostejov Years of Vilém Steinman
Prostějovská léta Viléma Steinmana

Ingrid Silná
2012 Musicologica Olomucensia  
Také oba jeho synové František Geisler (1819-1855) a Antonín Geisler (1821-1893) si zvolili učitelské povolání. Mladší syn Antonín působil na škole v Laškově a pak v Rokytnici u Přerova.  ...  Pavelka), vyučoval hudbě a podílel se pod vedením regenschoriho E. Ambrose na provádění chrámové hudby ve farním kostele Povýšení sv. Kříže.  ... 
doi:10.5507/mo.2012.013 fatcat:yv3aps7pr5fpdhcjvsa7xzas4u

Raisa Kuzněcovová a poznávání národní literatury: pohled z jiného úhlu a v širších souvislostech

Ivo Pospíšil, Institute of Slavonic Studies Masaryk University
2020 Stephanos Peer reviewed multilanguage scientific journal  
Antonín Měšťan zu seinem 65. Geburtstag. Herausgegeben von Prof. DrSc. Karel Mácha. Euroslavica, Prag 1996, a naši recenzi in: Opera Slavica, VII, 1997, 1, s. 67-69. 2 Viz J. Pavelka -I.  ...  Například René Wellek, po otci Čech, po matce polsko-italského původu, český a 1 O jeho vztahu k češtině a ruštině (Marina Cvetajevová) psal svého času český slavista Antonín Měšťan, emigré po roce 1968  ... 
doi:10.24249/2309-9917-2020-41-3-34-40 fatcat:y4kvse3xxfcwfisbqrf7iff6fa

NPDock: a web server for protein–nucleic acid docking

Irina Tuszynska, Marcin Magnus, Katarzyna Jonak, Wayne Dawson, Janusz M. Bujnicki
2015 Nucleic Acids Research  
ACKNOWLEDGEMENT The authors want to thank Antonin Pavelka, Joseph Yesselman and current and former members of the Bujnicki group, in particular Anna Philips, Wojciech Potrzebowski, Kristian Rother, Grzegorz  ... 
doi:10.1093/nar/gkv493 pmid:25977296 pmcid:PMC4489298 fatcat:puxxw5qne5etvbyj6la3jzczca
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