Radka Svobodová Vareková Coauthor index pubzone.org

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Radka Svobodová Vařeková

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j29Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLTomás Racek, Jana Pazúriková, Radka Svobodová Vareková, Stanislav Geidl, Ales Krenek, Francesco L. Falginella, Vladimír Horský, Václav Hejret, Jaroslav Koca: NEEMP: software for validation, accurate calculation and fast parameterization of EEM charges. J. Cheminformatics 8(1): 57:1-57:14 (2016)
j28Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLJon C. Ison, Kristoffer Rapacki, Hervé Ménager, Matús Kalas, Emil Rydza, Piotr Chmura, Christian Anthon, Niall Beard, Karel Berka, Dan M. Bolser, Tim Booth, Anthony Bretaudeau, Jan Brezovsky, Rita Casadio, Gianni Cesareni, Frederik Coppens, Michael Cornell, Gianmauro Cuccuru, Kristian Davidsen, Gianluca Della Vedova, Tunca Dogan, Olivia Doppelt-Azeroual, Laura Emery, Elisabeth Gasteiger, Thomas Gatter, Tatyana Goldberg, Marie Grosjean, Björn A. Grüning, Manuela Helmer-Citterich, Hans Ienasescu, Vassilios Ioannidis, Martin Closter Jespersen, Rafael C. Jimenez, Nick S. Juty, Peter Juvan, Maximilian Koch, Camille Laibe, Jing-Woei Li, Luana Licata, Fabien Mareuil, Ivan Micetic, Rune Møllegaard Friborg, Sébastien Moretti, Chris Morris, Steffen Möller, Aleksandra Nenadic, Hedi Peterson, Giuseppe Profiti, Peter M. Rice, Paolo Romano, Paola Roncaglia, Rabie Saidi, Andrea Schafferhans, Veit Schwämmle, Callum Smith, Maria Maddalena Sperotto, Heinz Stockinger, Radka Svobodová Vareková, Silvio C. E. Tosatto, Victor de la Torre, Paolo Uva, Allegra Via, Guy Yachdav, Federico Zambelli, Gert Vriend, Burkhard Rost, Helen E. Parkinson, Peter Løngreen, Søren Brunak: Tools and data services registry: a community effort to document bioinformatics resources. Nucleic Acids Research 44(Database-Issue): 38-47 (2016)
2015
j27Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLCrina-Maria Ionescu, David Sehnal, Francesco L. Falginella, Purbaj Pant, Lukás Pravda, Tomás Bouchal, Radka Svobodová Vareková, Stanislav Geidl, Jaroslav Koca: AtomicChargeCalculator: interactive web-based calculation of atomic charges in large biomolecular complexes and drug-like molecules. J. Cheminformatics 7: 50:1-50:13 (2015)
j26Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLStanislav Geidl, Tomás Bouchal, Tomás Racek, Radka Svobodová Vareková, Václav Hejret, Ales Krenek, Ruben Abagyan, Jaroslav Koca: High-quality and universal empirical atomic charges for chemoinformatics applications. J. Cheminformatics 7: 59:1-59:10 (2015)
j25Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLStanislav Geidl, Radka Svobodová Vareková, Veronika Bendová, Lukás Petrusek, Crina-Maria Ionescu, Zdenek Jurka, Ruben Abagyan, Jaroslav Koca: How Does the Methodology of 3D Structure Preparation Influence the Quality of pKa Prediction? Journal of Chemical Information and Modeling 55(6): 1088-1097 (2015)
j24Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLDavid Sehnal, Radka Svobodová Vareková, Lukás Pravda, Crina-Maria Ionescu, Stanislav Geidl, Vladimír Horský, Deepti Jaiswal, Michaela Wimmerová, Jaroslav Koca: ValidatorDB: database of up-to-date validation results for ligands and non-standard residues from the Protein Data Bank. Nucleic Acids Research 43(Database-Issue): 369-375 (2015)
j23Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLDavid Sehnal, Lukás Pravda, Radka Svobodová Vareková, Crina-Maria Ionescu, Jaroslav Koca: PatternQuery: web application for fast detection of biomacromolecular structural patterns in the entire Protein Data Bank. Nucleic Acids Research 43(Webserver-Issue): W383-W388 (2015)
2014
j22Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLLukás Pravda, Karel Berka, Radka Svobodová Vareková, David Sehnal, Pavel Banás, Roman A. Laskowski, Jaroslav Koca, Michal Otyepka: Anatomy of enzyme channels. BMC Bioinformatics 15: 379 (2014)
j21Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLDeepti Jaiswal, David Sehnal, Radka Svobodová Vareková, Crina-Maria Ionescu, Jaroslav Koca: Consistency of sugar structures and their annotation in the PDB. J. Cheminformatics 6(S-1): 41 (2014)
j20Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLTomás Bouchal, Radka Svobodová Vareková, Tomás Racek, Crina-Maria Ionescu, Stanislav Geidl, Ales Krenek, Jaroslav Koca: Empirical charges for chemoinformatics applications. J. Cheminformatics 6(S-1): 60 (2014)
j19Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLStanislav Geidl, Crina-Maria Ionescu, Radka Svobodová Vareková, Jaroslav Koca: QM quality atomic charges for proteins. J. Cheminformatics 6(S-1): 61 (2014)
j18Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLRadka Svobodová Vareková, Deepti Jaiswal, David Sehnal, Crina-Maria Ionescu, Stanislav Geidl, Lukás Pravda, Vladimír Horský, Michaela Wimmerová, Jaroslav Koca: MotiveValidator: interactive web-based validation of ligand and residue structure in biomolecular complexes. Nucleic Acids Research 42(Webserver-Issue): 227-233 (2014)
2013
j17Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLRadka Svobodová Vareková, Stanislav Geidl, Crina-Maria Ionescu, Ondrej Skrehota, Tomás Bouchal, David Sehnal, Ruben Abagyan, Jaroslav Koca: Predicting pKa values from EEM atomic charges. J. Cheminformatics 5: 18 (2013)
j16Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLDavid Sehnal, Radka Svobodová Vareková, Karel Berka, Lukás Pravda, Veronika Navrátilová, Pavel Banás, Crina-Maria Ionescu, Michal Otyepka, Jaroslav Koca: MOLE 2.0: advanced approach for analysis of biomacromolecular channels. J. Cheminformatics 5: 39 (2013)
j15Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLCrina-Maria Ionescu, Stanislav Geidl, Radka Svobodová Vareková, Jaroslav Koca: Rapid Calculation of Accurate Atomic Charges for Proteins via the Electronegativity Equalization Method. Journal of Chemical Information and Modeling 53(10): 2548-2558 (2013)
2012
j14Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLOndrej Skrehota, Radka Svobodová Vareková, Stanislav Geidl, Michal Kudera, David Sehnal, Crina-Maria Ionescu, Jan Zidek, Jaroslav Koca: QSPR designer - employ your own descriptors in the automated QSAR modeling process. J. Cheminformatics 4(S-1): 37 (2012)
j13Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLDavid Sehnal, Radka Svobodová Vareková, Heinrich J. Huber, Stanislav Geidl, Crina-Maria Ionescu, Michaela Wimmerová, Jaroslav Koca: SiteBinder - an improved approach for comparing multiple protein structural motifs. Case studies on biologically important motifs. J. Cheminformatics 4(S-1): 59 (2012)
j12Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLDeepti Jaiswal, Radka Svobodová Vareková, Crina-Maria Ionescu, David Sehnal, Jaroslav Koca: Searching for tunnels of proteins - comparison of approaches and available software tools. J. Cheminformatics 4(S-1): 60 (2012)
j11Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLStanislav Geidl, Roman Beránek, Radka Svobodová Vareková, Tomás Bouchal, Miroslav Brumovský, Michal Kudera, Ondrej Skrehota, Jaroslav Koca: How the methodology of 3D structure preparation influences the quality of QSPR models? J. Cheminformatics 4(S-1): 61 (2012)
j10Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLDavid Sehnal, Radka Svobodová Vareková, Heinrich J. Huber, Stanislav Geidl, Crina-Maria Ionescu, Michaela Wimmerová, Jaroslav Koca: SiteBinder: An Improved Approach for Comparing Multiple Protein Structural Motifs. Journal of Chemical Information and Modeling 52(2): 343-359 (2012)
j9Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLKarel Berka, Ondrej Hanák, David Sehnal, Pavel Banás, Veronika Navrátilová, Deepti Jaiswal, Crina-Maria Ionescu, Radka Svobodová Vareková, Jaroslav Koca, Michal Otyepka: MOLEonline 2.0: interactive web-based analysis of biomacromolecular channels. Nucleic Acids Research 40(Web-Server-Issue): 222-227 (2012)
j8Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLCrina-Maria Ionescu, Radka Svobodová Vareková, Jochen H. M. Prehn, Heinrich J. Huber, Jaroslav Koca: Charge Profile Analysis Reveals That Activation of Pro-apoptotic Regulators Bax and Bak Relies on Charge Transfer Mediated Allosteric Regulation. PLoS Computational Biology 8(6) (2012)
2011
j7Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLOndrej Skrehota, Radka Svobodová Vareková, Stanislav Geidl, Michal Kudera, David Sehnal, Crina-Maria Ionescu, Jaroslav Koca: QSPR designer - a program to design and evaluate QSPR models. Case study on pKa prediction. J. Cheminformatics 3(S-1): 16 (2011)
j6Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLRadka Svobodová Vareková, Stanislav Geidl, Crina-Maria Ionescu, Ondrej Skrehota, Michal Kudera, David Sehnal, Tomás Bouchal, Ruben Abagyan, Heinrich J. Huber, Jaroslav Koca: Predicting pKa Values of Substituted Phenols from Atomic Charges: Comparison of Different Quantum Mechanical Methods and Charge Distribution Schemes. Journal of Chemical Information and Modeling 51(8): 1795-1806 (2011)
2009
j5Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLZuzana Jirousková, Radka Svobodová Vareková, Jakub Vanek, Jaroslav Koca: Software news and updates electronegativity equalization method: Parameterization and validation for organic molecules using the Merz-Kollman-Singh charge distribution scheme. Journal of Computational Chemistry 30(7): 1174-1178 (2009)
2008
j4Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLRadka Svobodová Vareková, Ivan Bradác, Martin Plchút, Michal Skrdla, Michael Wacenovsky, Helmuth Mahr, Georg Mayer, Herbert Tanner, Hermann Brugger, Josef Withalm, Peter Lederer, Heinrich J. Huber, Gerhard Gierlinger, Ronald Graf, Hakim Tafer, Ivo L. Hofacker, Peter Schuster, Martin Polcík: www.rnaworkbench.com: A new program for analyzing RNA interference. Computer Methods and Programs in Biomedicine 90(1): 89-94 (2008)
j3Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLFergal P. Casey, Norman E. Davey, Ivan Baran, Radka Svobodová Vareková, Denis C. Shields: Web Server To Identify Similarity of Amino Acid Motifs to Compounds (SAAMCO). Journal of Chemical Information and Modeling 48(7): 1524-1529 (2008)
2007
j2Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLIvan Baran, Radka Svobodová Vareková, Laavanya Parthasarathi, Simon Suchomel, Fergal P. Casey, Denis C. Shields: Identification of Potential Small Molecule Peptidomimetics Similar to Motifs in Proteins. Journal of Chemical Information and Modeling 47(2): 464-474 (2007)
2006
j1Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLRadka Svobodová Vareková, Jaroslav Koca: Optimized and parallelized implementation of the electronegativity equalization method and the atom-bond electronegativity equalization method. Journal of Computational Chemistry 27(3): 396-405 (2006)

Coauthor Index

1Ruben Abagyan[j26] [j25] [j17] [j6]
2Christian Anthon[j28]
3Pavel Banás[j22] [j16] [j9]
4Ivan Baran[j3] [j2]
5Niall Beard[j28]
6Veronika Bendová[j25]
7Roman Beránek[j11]
8Karel Berka[j28] [j22] [j16] [j9]
9Dan M. Bolser[j28]
10Tim Booth[j28]
11Tomás Bouchal[j27] [j26] [j20] [j17] [j11] [j6]
12Ivan Bradác[j4]
13Anthony Bretaudeau[j28]
14Jan Brezovsky[j28]
15Hermann Brugger[j4]
16Miroslav Brumovský[j11]
17Søren Brunak[j28]
18Rita Casadio[j28]
19Fergal P. Casey[j3] [j2]
20Gianni Cesareni[j28]
21Piotr Chmura[j28]
22Frederik Coppens[j28]
23Michael Cornell[j28]
24Gianmauro Cuccuru[j28]
25Norman E. Davey[j3]
26Kristian Davidsen[j28]
27Tunca Dogan[j28]
28Olivia Doppelt-Azeroual[j28]
29Laura Emery[j28]
30Francesco L. Falginella[j29] [j27]
31Rune Møllegaard Friborg[j28]
32Elisabeth Gasteiger[j28]
33Thomas Gatter[j28]
34Stanislav Geidl[j29] [j27] [j26] [j25] [j24] [j20] [j19] [j18] [j17] [j15] [j14] [j13] [j11] [j10] [j7] [j6]
35Gerhard Gierlinger[j4]
36Tatyana Goldberg[j28]
37Ronald Graf[j4]
38Marie Grosjean[j28]
39Björn A. Grüning[j28]
40Ondrej Hanák[j9]
41Václav Hejret[j29] [j26]
42Manuela Helmer-Citterich[j28]
43Ivo L. Hofacker[j4]
44Vladimír Horský[j29] [j24] [j18]
45Heinrich J. Huber[j13] [j10] [j8] [j6] [j4]
46Hans Ienasescu[j28]
47Vassilios Ioannidis[j28]
48Crina-Maria Ionescu[j27] [j25] [j24] [j23] [j21] [j20] [j19] [j18] [j17] [j16] [j15] [j14] [j13] [j12] [j10] [j9] [j8] [j7] [j6]
49Jon C. Ison[j28]
50Deepti Jaiswal[j24] [j21] [j18] [j12] [j9]
51Martin Closter Jespersen[j28]
52Rafael C. Jimenez[j28]
53Zuzana Jirousková[j5]
54Zdenek Jurka[j25]
55Nick S. Juty[j28]
56Peter Juvan[j28]
57Matús Kalas[j28]
58Jaroslav Koca[j29] [j27] [j26] [j25] [j24] [j23] [j22] [j21] [j20] [j19] [j18] [j17] [j16] [j15] [j14] [j13] [j12] [j11] [j10] [j9] [j8] [j7] [j6] [j5] [j1]
59Maximilian Koch[j28]
60Ales Krenek[j29] [j26] [j20]
61Michal Kudera[j14] [j11] [j7] [j6]
62Camille Laibe[j28]
63Roman A. Laskowski[j22]
64Peter Lederer[j4]
65Jing-Woei Li[j28]
66Luana Licata[j28]
67Peter Løngreen[j28]
68Helmuth Mahr[j4]
69Fabien Mareuil[j28]
70Georg Mayer[j4]
71Hervé Ménager[j28]
72Ivan Micetic[j28]
73Steffen Möller[j28]
74Sébastien Moretti[j28]
75Chris Morris[j28]
76Veronika Navrátilová[j16] [j9]
77Aleksandra Nenadic[j28]
78Michal Otyepka[j22] [j16] [j9]
79Purbaj Pant[j27]
80Helen E. Parkinson[j28]
81Laavanya Parthasarathi[j2]
82Jana Pazúriková[j29]
83Hedi Peterson[j28]
84Lukás Petrusek[j25]
85Martin Plchút[j4]
86Martin Polcík[j4]
87Lukás Pravda[j27] [j24] [j23] [j22] [j18] [j16]
88Jochen H. M. Prehn[j8]
89Giuseppe Profiti[j28]
90Tomás Racek[j29] [j26] [j20]
91Kristoffer Rapacki[j28]
92Peter M. Rice[j28]
93Paolo Romano 0001[j28]
94Paola Roncaglia[j28]
95Burkhard Rost[j28]
96Emil Rydza[j28]
97Rabie Saidi[j28]
98Andrea Schafferhans[j28]
99Peter Schuster[j4]
100Veit Schwämmle[j28]
101David Sehnal[j27] [j24] [j23] [j22] [j21] [j18] [j17] [j16] [j14] [j13] [j12] [j10] [j9] [j7] [j6]
102Denis C. Shields[j3] [j2]
103Michal Skrdla[j4]
104Ondrej Skrehota[j17] [j14] [j11] [j7] [j6]
105Callum Smith[j28]
106Maria Sperotto
Maria Maddalena Sperotto
[j28]
107Heinz Stockinger[j28]
108Simon Suchomel[j2]
109Hakim Tafer[j4]
110Herbert Tanner[j4]
111Victor de la Torre[j28]
112Silvio C. E. Tosatto[j28]
113Paolo Uva[j28]
114Jakub Vanek[j5]
115Gianluca Della Vedova[j28]
116Allegra Via[j28]
117Gert Vriend[j28]
118Michael Wacenovsky[j4]
119Michaela Wimmerová[j24] [j18] [j13] [j10]
120Josef Withalm[j4]
121Guy Yachdav[j28]
122Federico Zambelli[j28]
123Jan Zidek[j14]

 

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