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1

Software news and updates electronegativity equalization method: Parameterization and validation for organic molecules using the Merz-Kollman-Singh charge distribution scheme

Zuzana Jiroušková, Radka Svobodová Vařeková, Jakub Vaněk, Jaroslav Koča

Journal:

Journal of Computational Chemistry

Year:

2009

Language:

english

File:

PDF, 79 KB

english, 2009

2

Muscular and neuromuscular control following soccer-specific exercise in male youth: Changes in injury risk mechanisms

Lehnert, M., De Ste Croix, M., Zaatar, A., Hughes, J., Varekova, R., Lastovicka, O.

Journal:

Scandinavian Journal of Medicine & Science in Sports

Year:

2016

Language:

english

File:

PDF, 176 KB

english, 2016

3

[IEEE 2018 IEEE 14th International Conference on e-Science (e-Science) - Amsterdam (2018.10.29-2018.11.1)] 2018 IEEE 14th International Conference on e-Science (e-Science) - Lesson Development for Open Source Software Best Practices Adoption

Kuzak, Mateusz, Harrow, Jen, Jimenez, Rafael C., Martinez, Paula Andrea, Psomopoulos, Fotis E., Svobodova Varekova, Radka, Via, Allegra

Year:

2018

Language:

english

File:

PDF, 6 KB

english, 2018

4

Optimized and parallelized implementation of the electronegativity equalization method and the atom-bond electronegativity equalization method

R. Svobodová Vařeková, J. Koča

Journal:

Journal of Computational Chemistry

Year:

2006

Language:

english

File:

PDF, 258 KB

english, 2006

5

Evaluation of Postural Asymmetry and Gross Joint Mobility in Elite Female Volleyball Athletes

Vařeková, Renata, Vařeka, Ivan, Janura, Miroslav, Svoboda, Zdenek, Elfmark, Milan

Journal:

Journal of Human Kinetics

Year:

2011

Language:

english

File:

PDF, 576 KB

english, 2011

6

[SpringerBriefs in Biochemistry and Molecular Biology] Structural Bioinformatics Tools for Drug Design ||

Koča, Jaroslav, Svobodová Vařeková, Radka, Pravda, Lukáš, Berka, Karel, Geidl, Stanislav, Sehnal, David, Otyepka, Michal

Year:

2016

Language:

english

File:

PDF, 6.72 MB

english, 2016

7

Real-Time Interactive Visualisation of Large Macromolecular Assemblies and Molecular Machines at Atomic Resolution

Sehnal, David, Deshpande, Mandar, Svobodova Varekova, Radka, Mir, Saquib, Berka, Karel, Midlik, Adam, Pravda, Lukas, Velankar, Sameer, Koca, Jaroslav

Journal:

Biophysical Journal

Year:

2017

Language:

english

File:

PDF, 47 KB

english, 2017

8

Worldwide Protein Data Bank validation information: usage and trends

Smart, Oliver S., Horský, Vladimír, Gore, Swanand, Svobodová Vařeková, Radka, Bendová, Veronika, Kleywegt, Gerard J., Velankar, Sameer

Journal:

Acta Crystallographica Section D Structural Biology

Year:

2018

Language:

english

File:

PDF, 1.01 MB

english, 2018

9

Changes in Injury Risk Mechanisms After Soccer-Specific Fatigue in Male Youth Soccer Players

Lehnert, Michal, Croix, Mark De Ste, Xaverova, Zuzana, Botek, Michal, Varekova, Renata, Zaatar, Amr, Lastovicka, Ondrej, Stastny, Petr

Journal:

Journal of Human Kinetics

Year:

2018

Language:

english

File:

PDF, 309 KB

english, 2018

10

Interactive 3D Macromolecular Structure Data Mining with MolQL and Litemol Suite

Sehnal, David, Deshpande, Mandar, Rose, Alexander, Pravda, Lukas, Midlik, Adam, Svobodová Vařeková, Radka, Mir, Saqib, Berka, Karel, Velankar, Sameer, Koca, Jaroslav

Journal:

Biophysical Journal

Year:

2018

Language:

english

File:

PDF, 44 KB

english, 2018

11

SugarSketcher: Quick and Intuitive Online Glycan Drawing

Alocci, Davide, Suchánková, Pavla, Costa, Renaud, Hory, Nicolas, Mariethoz, Julien, Vařeková, Radka, Toukach, Philip, Lisacek, Frédérique

Journal:

Year:

2018

Language:

english

File:

PDF, 1.46 MB

english, 2018

12

Effect of COL5A1, GDF5, and PPARA Genes on a Movement Screen and Neuromuscular Performance in Adolescent Team Sport Athletes

Stastny, Petr, Lehnert, Michal, De Ste Croix, Mark, Petr, Miroslav, Svoboda, Zdenek, Maixnerova, Eliska, Varekova, Renata, Botek, Michal, Petrek, Martin, Kocourkova, Lenka, Cięszczyk, Pawel

Journal:

The Journal of Strength and Conditioning Research

Year:

2019

File:

PDF, 507 KB

2019

13

A Case Study in Parallel Verification of Component-Based Systems

N. Beneš, I. Černá, J. Sochor, P. Vařeková, B. Zimmerova

Journal:

Electronic Notes in Theoretical Computer Science

Year:

2008

Language:

english

File:

PDF, 453 KB

english, 2008

14

Component Substitutability via Equivalencies of Component-Interaction Automata

Ivana Černá, Pavlína Vařeková, Barbora Zimmerova

Journal:

Electronic Notes in Theoretical Computer Science

Year:

2007

Language:

english

File:

PDF, 459 KB

english, 2007

15

Automated Computing of the Maximal Number of Handled Clients for Client-Server Systems

P. Vařeková, I. Vařeková, I. Černá

Journal:

Electronic Notes in Theoretical Computer Science

Year:

2010

Language:

english

File:

PDF, 425 KB

english, 2010

16

Partial order reduction for state/event LTL with application to component-interaction automata

N. Beneš, L. Brim, B. Buhnova, I. Černá, J. Sochor, P. Vařeková

Journal:

Science of Computer Programming

Year:

2011

Language:

english

File:

PDF, 546 KB

english, 2011

17

QSPR designer – a program to design and evaluate QSPR models. Case study on pKaprediction

O Skřehota, RS Vařeková, S Geidl, M Kudera, D Sehnal, C-M Ionescu, J Koča

Journal:

Journal of Cheminformatics

Year:

2011

Language:

english

File:

PDF, 168 KB

english, 2011

18

www.rnaworkbench.com: A new program for analyzing RNA interference

Radka Svobodová Vařeková, Ivan Bradáč, Martin Plchút, Michal Škrdla, Michael Wacenovsky, Helmuth Mahr, Georg Mayer, Herbert Tanner, Hermann Brugger, Josef Withalm, Peter Lederer, Heinrich Huber, Gerha

Journal:

Computer Methods and Programs in Biomedicine

Year:

2008

Language:

english

File:

PDF, 516 KB

english, 2008

19

Formal verification of systems with an unlimited number of components

Varekova, P., Zimmerova, B., Moravec, P., Cerna, I.

Journal:

Year:

2008

Language:

english

File:

PDF, 470 KB

english, 2008

20

QSPR designer – employ your own descriptors in the automated QSAR modeling process

Ondřej Skřehota, Radka Svobodová Vařeková, Stanislav Geidl, Michal Kudera, David Sehnal, Crina-Maria Ionescu, Jan Žídek, Jaroslav Koča

Journal:

Journal of Cheminformatics

Year:

2012

Language:

english

File:

PDF, 74 KB

english, 2012

21

Searching for tunnels of proteins – comparison of approaches and available software tools

Deepti Jaiswal, Radka Svobodová Vařeková, Crina-Maria Ionescu, David Sehnal, Jaroslav Koča

Journal:

Journal of Cheminformatics

Year:

2012

Language:

english

File:

PDF, 72 KB

english, 2012

22

SiteBinder – an improved approach for comparing multiple protein structural motifs. Case studies on biologically important motifs

David Sehnal, Radka Svobodová Vařeková, Heinrich J Huber, Stanislav Geidl, Crina-Maria Ionescu, Michaela Wimmerová, Jaroslav Koča

Journal:

Journal of Cheminformatics

Year:

2012

Language:

english

File:

PDF, 75 KB

english, 2012

23

How the methodology of 3D structure preparation influences the quality of QSPR models?

Stanislav Geidl, Roman Beránek, Radka Svobodová Vařeková, Tomáš Bouchal, Miroslav Brumovský, Michal Kudera, Ondřej Skřehota, Jaroslav Koča

Journal:

Journal of Cheminformatics

Year:

2012

Language:

english

File:

PDF, 72 KB

english, 2012

24

siRNA selection criteria—Statistical analyses of applicability and significance

Ivan Bradáč, Radka Svobodová Vařeková, Michael Wacenovsky, Michal Škrdla, Martin Plchút, Martin Polčík

Journal:

Biochemical and Biophysical Research Communications

Year:

2007

Language:

english

File:

PDF, 269 KB

english, 2007

25

MOLE 2.0: advanced approach for analysis of biomacromolecular channels

Sehnal, David, Svobodová Vařeková, Radka, Berka, Karel, Pravda, Lukáš, Navrátilová, Veronika, Banáš, Pavel, Ionescu, Crina-Maria, Otyepka, Michal, Koča, Jaroslav

Journal:

Journal of Cheminformatics

Year:

2013

Language:

english

File:

PDF, 1.45 MB

english, 2013

26

How to estimate overweight in pubescent asthmatics?

Varekova, R, Vareka, I

Journal:

Advances in Medical Sciences

Year:

2013

Language:

english

File:

PDF, 316 KB

english, 2013

27

QM quality atomic charges for proteins

Geidl, Stanislav, Ionescu, Crina-Maria, Vařeková, Radka, Koča, Jaroslav

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 73 KB

english, 2014

28

Consistency of sugar structures and their annotation in the PDB

Jaiswal, Deepti, Sehnal, David, Vařeková, Radka, Ionescu, Crina-Maria, Koča, Jaroslav

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 74 KB

english, 2014

29

Empirical charges for chemoinformatics applications

Bouchal, Tomáš, Vařeková, Radka, Raček, Tomáš, Ionescu, Crina-Maria, Geidl, Stanislav, Křenek, Aleš, Koča, Jaroslav

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 73 KB

english, 2014

30

SiteBinder: An Improved Approach for Comparing Multiple Protein Structural Motifs

Sehnal, David, Vařeková, Radka Svobodová, Huber, Heinrich J., Geidl, Stanislav, Ionescu, Crina-Maria, Wimmerová, Michaela, Koča, Jaroslav

Journal:

Journal of Chemical Information and Modeling

Year:

2012

Language:

english

File:

PDF, 5.57 MB

english, 2012

31

Rapid Calculation of Accurate Atomic Charges for Proteins via the Electronegativity Equalization Method

Ionescu, Crina-Maria, Geidl, Stanislav, Svobodová Vařeková, Radka, Koča, Jaroslav

Journal:

Journal of Chemical Information and Modeling

Year:

2013

Language:

english

File:

PDF, 579 KB

english, 2013

32

Runtime analysis of probabilistic programs with unbounded recursion

Brázdil, Tomáš, Kiefer, Stefan, Kučera, Antonín, Hutařová Vařeková, Ivana

Journal:

Journal of Computer and System Sciences

Year:

2015

Language:

english

File:

PDF, 587 KB

english, 2015

33

Identification of Potential Small Molecule Peptidomimetics Similar to Motifs in Proteins

Baran, Ivan, Varekova, Radka Svobodova, Parthasarathi, Laavanya, Suchomel, Simon, Casey, Fergal, Shields, Denis C.

Journal:

Journal of Chemical Information and Modeling

Year:

2007

Language:

english

File:

PDF, 492 KB

english, 2007

34

Web Server To Identify Similarity of Amino Acid Motifs to Compounds (SAAMCO)

Casey, Fergal P., Davey, Norman E., Baran, Ivan, Varekova, Radka Svobodova, Shields, Denis C.

Journal:

Journal of Chemical Information and Modeling

Year:

2008

Language:

english

File:

PDF, 2.15 MB

english, 2008

35

Anatomy of enzyme channels

Pravda, Lukáš, Berka, Karel, Svobodová Vařeková, Radka, Sehnal, David, Banáš, Pavel, Laskowski, Roman A, Koča, Jaroslav, Otyepka, Michal

Journal:

BMC Bioinformatics

Year:

2014

Language:

english

File:

PDF, 891 KB

english, 2014

36

Characterization of Staphylococcus aureus Strains Isolated from Czech Cystic Fibrosis Patients: High Rate of Ribosomal Mutation Conferring Resistance to MLS B Antibiotics as a Result of Long-Term and Low-Dose Azithromycin Treatment

Tkadlec, Jan, Vařeková, Eva, Pantůček, Roman, Doškař, Jiří, Růžičková, Vladislava, Botka, Tibor, Fila, Libor, Melter, Oto

Journal:

Microbial Drug Resistance

Year:

2015

Language:

english

File:

PDF, 215 KB

english, 2015

37

How Does the Methodology of 3D Structure Preparation Influence the Quality of p K a Prediction?

Geidl, Stanislav, Svobodová Vařeková, Radka, Bendová, Veronika, Petrusek, Lukáš, Ionescu, Crina-Maria, Jurka, Zdeněk, Abagyan, Ruben, Koča, Jaroslav

Journal:

Journal of Chemical Information and Modeling

Year:

2015

Language:

english

File:

PDF, 530 KB

english, 2015

38

Charge Profile Analysis Reveals That Activation of Pro-apoptotic Regulators Bax and Bak Relies on Charge Transfer Mediated Allosteric Regulation

Ionescu, Crina-Maria, Svobodová Vařeková, Radka, Prehn, Jochen H. M., Huber, Heinrich J., Koča, Jaroslav, Briggs, James M.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 757 KB

english, 2012

39

[ACM Press the 2007 conference - Dubrovnik, Croatia (2007.09.03-2007.09.04)] Proceedings of the 2007 conference on Specification and verification of component-based systems 6th Joint Meeting of the European Conference on Software Engineering and the ACM SIGSOFT Symposium on the Foundations of Software Engineering - SAVCBS '07 - Subject-observer specification with component-interaction automata

Vařeková, Pavlína, Zimmerova, Barbora

Year:

2007

Language:

english

File:

PDF, 386 KB

english, 2007

40

[ACM Press the 2005 conference - Lisbon, Portugal (2005.09.05-2005.09.06)] Proceedings of the 2005 conference on Specification and verification of component-based systems - SAVCBS '05 - Component-interaction automata as a verification-oriented component-based system specification

Brim, Luboš, Černá, Ivana, Vařeková, Pavlína, Zimmerova, Barbora

Year:

2005

Language:

english

File:

PDF, 181 KB

english, 2005

41

MOLEonline 2.0: interactive web-based analysis of biomacromolecular channels

Berka, K., Hanak, O., Sehnal, D., Banas, P., Navratilova, V., Jaiswal, D., Ionescu, C.-M., Svobodova Varekova, R., Koca, J., Otyepka, M.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 7.25 MB

english, 2012

42

[ACM Press the 2007 conference - Dubrovnik, Croatia (2007.09.03-2007.09.04)] Proceedings of the 2007 conference on Specification and verification of component-based systems 6th Joint Meeting of the European Conference on Software Engineering and the ACM SIGSOFT Symposium on the Foundations of Software Engineering - SAVCBS '07 - Effective verification of systems with a dynamic number of components

Vařeková, Pavlína, Moravec, Pavel, Černá, Ivana, Zimmerova, Barbora

Year:

2007

Language:

english

File:

PDF, 557 KB

english, 2007

43

AtomicChargeCalculator: interactive web-based calculation of atomic charges in large biomolecular complexes and drug-like molecules

Ionescu, Crina-Maria, Sehnal, David, Falginella, Francesco L., Pant, Purbaj, Pravda, Lukáš, Bouchal, Tomáš, Svobodová Vařeková, Radka, Geidl, Stanislav, Koča, Jaroslav

Journal:

Journal of Cheminformatics

Year:

2015

Language:

english

File:

PDF, 2.67 MB

english, 2015

44

High-quality and universal empirical atomic charges for chemoinformatics applications

Geidl, Stanislav, Bouchal, Tomáš, Raček, Tomáš, Svobodová Vařeková, Radka, Hejret, Václav, Křenek, Aleš, Abagyan, Ruben, Koča, Jaroslav

Journal:

Journal of Cheminformatics

Year:

2015

Language:

english

File:

PDF, 1.32 MB

english, 2015

45

PatternQuery: web application for fast detection of biomacromolecular structural patterns in the entire Protein Data Bank

Sehnal, David, Pravda, Lukáš, Svobodová Vařeková, Radka, Ionescu, Crina-Maria, Koča, Jaroslav

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.09 MB

english, 2015

46

Component-interaction automata as a verification-oriented component-based system specification

Brim, Luboš, Černá, Ivana, Vařeková, Pavlína, Zimmerova, Barbora

Journal:

ACM SIGSOFT Software Engineering Notes

Year:

2006

Language:

english

File:

PDF, 181 KB

english, 2006

47

NEEMP: software for validation, accurate calculation and fast parameterization of EEM charges

Raček, Tomáš, Pazúriková, Jana, Svobodová Vařeková, Radka, Geidl, Stanislav, Křenek, Aleš, Falginella, Francesco Luca, Horský, Vladimír, Hejret, Václav, Koča, Jaroslav

Journal:

Journal of Cheminformatics

Year:

2016

Language:

english

File:

PDF, 2.95 MB

english, 2016

48

[SpringerBriefs in Biochemistry and Molecular Biology] Structural Bioinformatics Tools for Drug Design || Detection of Channels

Koča, Jaroslav, Svobodová Vařeková, Radka, Pravda, Lukáš, Berka, Karel, Geidl, Stanislav, Sehnal, David, Otyepka, Michal

Year:

2016

Language:

english

File:

PDF, 603 KB

english, 2016

49

[SpringerBriefs in Biochemistry and Molecular Biology] Structural Bioinformatics Tools for Drug Design || Biomacromolecular Fragments and Patterns

Koča, Jaroslav, Svobodová Vařeková, Radka, Pravda, Lukáš, Berka, Karel, Geidl, Stanislav, Sehnal, David, Otyepka, Michal

Year:

2016

Language:

english

File:

PDF, 377 KB

english, 2016

50

Mole 2.5 - Tool for Detection and Analysis of Macromolecular Pores and Channels

Berka, Karel, Sehnal, David, Bazgier, Vaclav, Pravda, Lukas, Svobodova-Varekova, Radka, Otyepka, Michal, Koca, Jaroslav

Journal:

Biophysical Journal

Year:

2017

Language:

english

File:

PDF, 61 KB

english, 2017