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Crina-Maria Ionescu
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2020 – today
- 2023
- [j21]Aliaksei Chareshneu
, Adam Midlik
, Crina-Maria Ionescu, Alexander S. Rose
, Vladimír Horský
, Alessio Cantara, Radka Svobodová Vareková
, Karel Berka
, David Sehnal:
Mol* Volumes and Segmentations: visualization and interpretation of cell imaging data alongside macromolecular structure data and biological annotations. Nucleic Acids Res. 51(W1): 326-330 (2023)
2010 – 2019
- 2017
- [j20]Ravi José Tristão Ramos, Allan Cézar de Azevedo Martins
, Gabrielle da Silva Delgado, Crina-Maria Ionescu, Turán Peter Ürményi, Rosane Silva
, Jaroslav Koca
:
CrocoBLAST: Running BLAST efficiently in the age of next-generation sequencing. Bioinform. 33(22): 3648-3651 (2017) - 2015
- [j19]Crina-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) - [j18]Stanislav 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? J. Chem. Inf. Model. 55(6): 1088-1097 (2015) - [j17]David Sehnal
, Radka Svobodová Vareková
, Lukás Pravda
, Crina-Maria Ionescu, Stanislav Geidl, Vladimír Horský
, Deepti Jaiswal Kundu
, 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 Res. 43(Database-Issue): 369-375 (2015) - [j16]David 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 Res. 43(Webserver-Issue): W383-W388 (2015) - 2014
- [j15]Deepti Jaiswal Kundu
, 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) - [j14]Tomás 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) - [j13]Stanislav Geidl, Crina-Maria Ionescu, Radka Svobodová Vareková, Jaroslav Koca:
QM quality atomic charges for proteins. J. Cheminformatics 6(S-1): 61 (2014) - [j12]Radka Svobodová Vareková
, Deepti Jaiswal Kundu
, 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 Res. 42(Webserver-Issue): 227-233 (2014) - 2013
- [j11]Radka 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) - [j10]David 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) - [j9]Crina-Maria Ionescu, Stanislav Geidl, Radka Svobodová Vareková
, Jaroslav Koca
:
Rapid Calculation of Accurate Atomic Charges for Proteins via the Electronegativity Equalization Method. J. Chem. Inf. Model. 53(10): 2548-2558 (2013) - 2012
- [j8]Ondrej 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) - [j7]David 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) - [j6]Deepti Jaiswal Kundu, 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) - [j5]David 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. J. Chem. Inf. Model. 52(2): 343-359 (2012) - [j4]Karel Berka
, Ondrej Hanák, David Sehnal
, Pavel Banás, Veronika Navrátilová, Deepti Jaiswal Kundu
, Crina-Maria Ionescu, Radka Svobodová Vareková
, Jaroslav Koca
, Michal Otyepka
:
MOLEonline 2.0: interactive web-based analysis of biomacromolecular channels. Nucleic Acids Res. 40(Web-Server-Issue): 222-227 (2012) - [j3]Crina-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 Comput. Biol. 8(6) (2012) - 2011
- [j2]Ondrej 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) - [j1]Radka 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. J. Chem. Inf. Model. 51(8): 1795-1806 (2011)
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