Výpis publikací

CHARESHNEU, Aliaksei, Adam MIDLIK, Crina-Maria IONESCU, Alexander ROSE, Vladimír HORSKÝ, Alessio CANTARA, Radka SVOBODOVÁ, Karel BERKA a David SEHNAL. Mol* Volumes and Segmentations: visualization and interpretation of cell imaging data alongside macromolecular structure data and biological annotations. Nucleic Acids Research. Oxford University Press, 2023, roč. 51, W1, s. "W326"-"W330", 5 s. ISSN 0305-1048. Dostupné z: https://dx.doi.org/10.1093/nar/gkad411.

CHARESHNEU, Aliaksei, Purbaj PANT, Ravi José Tristao RAMOS, David SEHNAL, Tuğrul GÖKBEL, Crina-Maria IONESCU a Jaroslav KOČA. NAChRDB: A Web Resource of Structure–Function Annotations to Unravel the Allostery of Nicotinic Acetylcholine Receptors. ACS Omega. American Chemical Society, 2021, roč. 6, č. 36, s. 23023-23027. ISSN 2470-1343. Dostupné z: https://dx.doi.org/10.1021/acsomega.1c00817.

CHARESHNEU, Aliaksei, Purbaj PANT, Ravi José TRISTÃO RAMOS, David SEHNAL, Tuğrul GÖKBEL, Crina-Maria IONESCU a Jaroslav KOČA. NAChRDB: Interactive annotations to untangle allostery of nicotinic acetylcholine receptor. In VIZBI 2021 - 11th international meeting on Visualizing Biological Data. 2021.

CHARESHNEU, Aliaksei, Purbaj PANT, Ravi José Tristao RAMOS, David SEHNAL, Tuğrul GÖKBEL, Crina-Maria IONESCU a Jaroslav KOČA. NAChRDB: Solving the puzzle of structure-function relationships to clarify the allostery of nicotinic acetylcholine receptors (nAChRs). In 1st Student Conference in Structural Biology. 2021.

CHARESHNEU, Aliaksei, Purbaj PANT, Ravi José Tristao RAMOS, Tuğrul GÖKBEL, Crina-Maria IONESCU a Jaroslav KOČA. NACHRDB: Solving the puzzle of structure-function relationships in nicotinic acetylcholine receptors (nAChRs). In Neuronus IBRO Neuroscience Forum. 2020.

CHARESHNEU, Aliaksei, Purbaj PANT, Ravi José Tristao RAMOS, Tuğrul GÖKBEL, Crina-Maria IONESCU a Jaroslav KOČA. NACHRDB: Solving the puzzle of structure-function relationships in nicotinic acetylcholine receptors (nAChRs). In Book of Abstracts, Neuronus IBRO Neuroscience Forum. 2020.

CHARESHNEU, Aliaksei, Ravi José TRISTAO RAMOS, Crina-Maria IONESCU a Jaroslav KOČA. NACHRDB: Residue-level functional annotations of nicotinic acetylcholine receptors (nAChRs). In 7th Spanish-Italian-Portuguese-French International Workshop on Structure and Function of Ion Channels and Transporters. 2019.

CHARESHNEU, Aliaksei, Ravi José TRISTAO RAMOS, Crina-Maria IONESCU a Jaroslav KOČA. NACHRDB: Residue-level functional annotations of nicotinic acetylcholine receptors (nAChRs). In Book of Abstracts, 7th Spanish-Italian-Portuguese-French International Workshop on Structure and Function of Ion Channels and Transporters. 2019.

CHARESHNEU, Aliaksei, Ravi José Tristao RAMOS, Crina-Maria IONESCU a Jaroslav KOČA. NACHRDB: Solving the puzzle of structure-function relationships in nicotinic acetylcholine receptors (nAChRs). In 20th Meeting of Biochemists and Molecular Biologists. 2019.

CHARESHNEU, Aliaksei, Ravi José Tristao RAMOS, Crina-Maria IONESCU a Jaroslav KOČA. NACHRDB: Solving the puzzle of structure-function relationships in nicotinic acetylcholine receptors (nAChRs). In Book of Abstracts, 20th Meeting of Biochemists and Molecular Biologists. 2019.

CHARESHNEU, Aliaksei, Ravi José Tristao RAMOS, Crina-Maria IONESCU a Jaroslav KOČA. NACHRDB: Solving the puzzle of structure-function relationships in nicotinic acetylcholine receptors (nAChRs). In Book of Abstracts, 20th Meeting of Biochemists and Molecular Biologists. 2019.

CHARESHNEU, Aliaksei, Ravi José TRISTAO RAMOS, Crina-Maria IONESCU a Jaroslav KOČA. NACHRDB: Solving the puzzle of structure-function relationships in nicotinic acetylcholine receptors (nAChRs). In The Biomania Student Scientific Meeting & EUSynBioS Symposium 2019. 2019. ISBN 978-80-210-9373-7.

CHARESHNEU, Aliaksei, Ravi José TRISTAO RAMOS, Crina-Maria IONESCU a Jaroslav KOČA. NACHRDB: Solving the puzzle of structure-function relationships in nicotinic acetylcholine receptors (nAChRs). In Book of Abstracts, The Biomania Student Scientific Meeting & EUSynBioS Symposium 2019. 2019. ISBN 978-80-210-9373-7.

CHARESHNEU, Aliaksei, Ravi José Tristao RAMOS, Crina-Maria IONESCU a Jaroslav KOČA. NACHRDB: Unraveling the structure-function relationships in nicotinic acetylcholine receptors (nAChRs). In 11th EMBO Young Scientists Forum, Prague, Czech Republic. 2019.

CHARESHNEU, Aliaksei, Ravi José TRISTAO RAMOS, Crina-Maria IONESCU a Jaroslav KOČA. Structural bioinformatics of nicotinic acetylcholine receptors: NACHRDB. In Joint Retreat 2019. 2019. ISBN 978-80-210-9300-3.

CHARESHNEU, Aliaksei, Ravi José TRISTAO RAMOS, Crina-Maria IONESCU a Jaroslav KOČA. Structural bioinformatics of nicotinic acetylcholine receptors: NACHRDB. In Book of Abstracts, Joint Retreat 2019. 2019. ISBN 978-80-210-9300-3.

CHARESHNEU, Aliaksei, Purbaj PANT, Ravi José Tristao RAMOS, David SEHNAL, Tuğrul GÖKBEL, Crina-Maria IONESCU a Jaroslav KOČA. NAChRDB: Database of structural-functional annotations of nicotinic acetylcholine receptors. 2018.

TRISTAO RAMOS, Ravi José, Allan Cézar DE AZEVEDO MARTINS, Gabrielle DA SILVA DELGADO, Crina-Maria IONESCU, Peter Turán ÜRMÉNYI, Rosane SILVA a Jaroslav KOČA. CrocoBLAST: Running BLAST efficiently in the age of next-generation sequencing. Bioinformatics. Oxford: Oxford University Press, 2017, roč. 33, č. 22, s. 3648-3651. ISSN 1367-4803. Dostupné z: https://dx.doi.org/10.1093/bioinformatics/btx465.

PRAVDA, Lukáš, Karel BERKA, Radka SVOBODOVÁ VAŘEKOVÁ, David SEHNAL, Crina-Maria IONESCU, Michal OTYEPKA a Jaroslav KOČA. Anatomy of protein channels. In CEITEC PhD Retreat, Valtice, The Czech Republic. 2015. ISBN 978-80-210-7825-3.

IONESCU, Crina-Maria, David SEHNAL, Francesco Luca FALGINELLA, Purbaj PANT, Lukáš PRAVDA, Tomáš BOUCHAL, Radka SVOBODOVÁ VAŘEKOVÁ, Stanislav GEIDL a Jaroslav KOČA. AtomicChargeCalculator: Interactive Web-based calculation of atomic charges in large biomolecular complexes and drug like molecules. Journal of Cheminformatics. London: BIOMED CENTRAL LTD, 2015, roč. 7, č. 50, s. "nestránkováno", 13 s. ISSN 1758-2946. Dostupné z: https://dx.doi.org/10.1186/s13321-015-0099-x.

GEIDL, Stanislav, Radka SVOBODOVÁ VAŘEKOVÁ, Veronika BENDOVÁ, Lukáš PETRUSEK, Crina-Maria IONESCU, Zdeněk JURKA, Ruben A. ABAGYAN a Jaroslav KOČA. How Does the Methodology of 3D Structure Preparation Influence the Quality of pK(a) Prediction? Journal of Chemical Information and Modeling. WASHINGTON: AMER CHEMICAL SOC, 2015, roč. 55, č. 6, s. 1088-1097. ISSN 1549-9596. Dostupné z: https://dx.doi.org/10.1021/ci500758w.

SVOBODOVÁ VAŘEKOVÁ, Radka, Lukáš PRAVDA, David SEHNAL, Crina-Maria IONESCU a Jaroslav KOČA. MotiveQuery: Web application for fast detection of biomacromolecular fragments in the entire Protein Data Bank. In ISMB/ECCB 2015, Dublin, Ireland. 2015.

SEHNAL, David, Lukáš PRAVDA, Radka SVOBODOVÁ VAŘEKOVÁ, Crina-Maria IONESCU a Jaroslav KOČA. PatternQuery: web application for fast detection of biomacromolecular structural patterns in the entire Protein Data Bank. Nucleic Acids Research. Oxford: Oxford University Press, 2015, roč. 43, W1, s. "W383"-"W388", 6 s. ISSN 0305-1048. Dostupné z: https://dx.doi.org/10.1093/nar/gkv561.

PRAVDA, Lukáš, David SEHNAL, Radka SVOBODOVÁ VAŘEKOVÁ, Crina-Maria IONESCU a Jaroslav KOČA. PatternQuery: Web application for fast detection of biomacromolecular structural patterns in the entire Protein Data Bank. In 3Dsig meeting at ISMB/ECCB 2015, Dublin, Ireland. 2015.

SEHNAL, David, Radka SVOBODOVÁ VAŘEKOVÁ, Lukáš PRAVDA, Crina-Maria IONESCU, Stanislav GEIDL, Vladimír HORSKÝ, Deepti JAISWAL, Michaela WIMMEROVÁ a Jaroslav KOČA. ValidatorDB: database of up-to-date validation results for ligands and non-standard residues from the Protein Data Bank. Nucleic Acids Research. United Kingdom: Oxford University Press, 2015, roč. 43, D1, s. "D369"-"D375", 7 s. ISSN 0305-1048. Dostupné z: https://dx.doi.org/10.1093/nar/gku1118.

SVOBODOVÁ VAŘEKOVÁ, Radka, David SEHNAL, Lukáš PRAVDA, Crina-Maria IONESCU a Jaroslav KOČA. ValidatorDB: database of up-to-date validation results for ligands and non-standard residues from the Protein Data Bank. In 3Dsig meeting at ISMB/ECCB 2015, Dublin, Ireland. 2015.

SEHNAL, David, Lukáš PRAVDA, Crina-Maria IONESCU, Radka SVOBODOVÁ VAŘEKOVÁ a Jaroslav KOČA. WebChemistry: a platform for the detection, validation, comparison, and characterization of structural patterns in biomacromolecules. In ISMB/ECCB 2015, Dublin, Ireland. 2015.

PRAVDA, Lukáš, Radka SVOBODOVÁ VAŘEKOVÁ, David SEHNAL, Crina-Maria IONESCU, Karel BERKA, Michal OTYEPKA a Jaroslav KOČA. Anatomy of enzymatic channels and algorithm for its detection. In 13th European Conference on Computational Biology, Strasbourg, France. 2014.

SVOBODOVÁ VAŘEKOVÁ, Radka, Stanislav GEIDL, David SEHNAL, Lukáš PRAVDA, Zdeněk JURKA, Crina-Maria IONESCU a Jaroslav KOČA. Atomic charge based descriptors and their applications in QSAR. In 20th EuroQSAR - Understanding Chemical-Biological Interactions, St. Petersburg, Russia. 2014.

JAISWAL, Deepti, Radka SVOBODOVÁ VAŘEKOVÁ, David SEHNAL, Crina-Maria IONESCU, Stanislav GEIDL, Lukáš PRAVDA, Vladimír HORSKÝ, Michaela WIMMEROVÁ a Jaroslav KOČA. Consistency of sugar structures and their annotation in the PDB. In 13th European Conference on Computational Biology, Strasbourg, France. 2014.

GEIDL, Stanislav, Radka SVOBODOVÁ VAŘEKOVÁ, Lukáš PETRUSEK, Crina-Maria IONESCU, David SEHNAL a Jaroslav KOČA. How the methodology of 3D structure preparation influences the quality of pKa prediction? In 20th EuroQSAR - Understanding Chemical-Biological Interactions, St. Petersburg, Russia. 2014.

SEHNAL, David, Radka SVOBODOVÁ VAŘEKOVÁ, Crina-Maria IONESCU, Stanislav GEIDL, Lukáš PRAVDA, Deepti JAISWAL, Michaela WIMMEROVÁ a Jaroslav KOČA. Ligand structures in the Protein Data Bank – can we trust them? In 10th International Conference on Chemical Structures and 10th German Conference on Chemoinformatics, Noordwijkerhout, The Netherlands. 2014.

PRAVDA, Lukáš, Radka SVOBODOVÁ VAŘEKOVÁ, David SEHNAL, Crina-Maria IONESCU, Karel BERKA, Michal OTYEPKA a Jaroslav KOČA. MOLE: Pokročilý nástroj pro vyhledávání a charakterizaci tunelů. In ENBIK - Národní bioinformatická konference. 2014. ISBN 978-80-7080-883-2.

PRAVDA, Lukáš, Radka SVOBODOVÁ VAŘEKOVÁ, David SEHNAL, Crina-Maria IONESCU a Jaroslav KOČA. MotiveQuery: Language and Web Service for Fast Identification of Protein Structural Motifs in the Entire Protein Data Bank. In 10th International Conference on Chemical Structures and 10th German Conference on Chemoinformatics, Noordwijkerhout, The Netherlands. 2014.

SVOBODOVÁ VAŘEKOVÁ, Radka, Deepti JAISWAL, David SEHNAL, Crina-Maria IONESCU, Stanislav GEIDL, Lukáš PRAVDA, Vladimír HORSKÝ, Michaela WIMMEROVÁ a Jaroslav KOČA. MotiveValidator: interactive web-based validation of ligand and residue structure in biomolecular complexes. Nucleic Acids Research. Oxford, UK: Oxford University Press, 2014, roč. 42, W1, s. "W227"-"W233", 7 s. ISSN 0305-1048. Dostupné z: https://dx.doi.org/10.1093/nar/gku426.

SVOBODOVÁ VAŘEKOVÁ, Radka, Deepti JAISWAL, David SEHNAL, Crina-Maria IONESCU, Stanislav GEIDL, Lukáš PRAVDA, Vladimír HORSKÝ, Michaela WIMMEROVÁ a Jaroslav KOČA. MotiveValidator: software for validation of ligand and residue structures in biomolecular complexes. 2014.

SVOBODOVÁ VAŘEKOVÁ, Radka, Deepti JAISWAL, David SEHNAL, Crina-Maria IONESCU, Stanislav GEIDL, Lukáš PRAVDA, Vladimír HORSKÝ, Michaela WIMMEROVÁ a Jaroslav KOČA. ValidatorDB: database of validation results for ligands and non-standard residues from the Protein Data Bank. 2014.

GEIDL, Stanislav, David SEHNAL, Crina-Maria IONESCU, Radka SVOBODOVÁ VAŘEKOVÁ, Purbaj PANT a Jaroslav KOČA. Web server for the rapid calculation of empirical atomic charges with QM accuracy. In 10th International Conference on Chemical Structures and the 10th German Conference on Chemoinformatics. 2014.

BOUCHAL, Tomáš, Radka SVOBODOVÁ VAŘEKOVÁ, Tomáš RAČEK, Crina-Maria IONESCU, Stanislav GEIDL, Aleš KŘENEK a Jaroslav KOČA. Empirical charges for chemoinformatics applications. In GCC 2013 - 9th German Conference on Chemoinformatics. 2013. Dostupné z: https://dx.doi.org/10.1186/1758-2946-6-S1-P60.

SEHNAL, David, Radka SVOBODOVÁ VAŘEKOVÁ, Karel BERKA, Lukáš PRAVDA, Veronika NAVRÁTILOVÁ, Pavel BANÁŠ, Crina-Maria IONESCU, Michal OTYEPKA a Jaroslav KOČA. MOLE 2.0: advanced approach for analysis of biomacromolecular channels. Journal of Cheminformatics. London: BIOMED CENTRAL LTD, 2013, roč. 5, č. 39, s. "nestránkováno", 13 s. ISSN 1758-2946. Dostupné z: https://dx.doi.org/10.1186/1758-2946-5-39.

SVOBODOVÁ VAŘEKOVÁ, Radka, Stanislav GEIDL, Crina-Maria IONESCU, Ondřej SKŘEHOTA, Tomáš BOUCHAL, David SEHNAL, Ruben A. ABAGYAN a Jaroslav KOČA. Predicting pKa values from EEM atomic charges. Journal of Cheminformatics. London: BIOMED CENTRAL LTD, 2013, roč. 5, č. 18, s. "nestránkováno", 15 s. ISSN 1758-2946. Dostupné z: https://dx.doi.org/10.1186/1758-2946-5-18.

GEIDL, Stanislav, Crina-Maria IONESCU, Radka SVOBODOVÁ VAŘEKOVÁ a Jaroslav KOČA. QM quality atomic charges for proteins. In GCC 2013 - 9th German Conference on Chemoinformatics. 2013. Dostupné z: https://dx.doi.org/10.1186/1758-2946-6-S1-P61.

IONESCU, Crina-Maria, Stanislav GEIDL, Radka SVOBODOVÁ VAŘEKOVÁ a Jaroslav KOČA. Rapid Calculation of Accurate Atomic Charges for Proteins via the Electronegativity Equalization Method. Journal of Chemichal Information a Modeling. WASHINGTON: AMER CHEMICAL SOC, 2013, roč. 53, č. 10, s. 2548-2558. ISSN 1549-9596. Dostupné z: https://dx.doi.org/10.1021/ci400448n.

IONESCU, Crina-Maria, Zuzana KLÍMOVÁ, David SEHNAL, Radka SVOBODOVÁ VAŘEKOVÁ a Jaroslav KOČA. BH3-ONLY PROTEINS - FROM STRUCTURE TO FUNCTION. In XXIII. biochemický sjezd České společnosti pro biochemii a molekulární biologii a Slovenské spoločnosti pre biochémiu a molekulárnu biológiu. 2012.

IONESCU, Crina-Maria, Radka SVOBODOVÁ VAŘEKOVÁ, Jochen HM PREHN, Heinrich J HUBER a Jaroslav KOČA. Charge Profile Analysis Reveals That Activation of Pro-apoptotic Regulators Bax and Bak Relies on Charge Transfer Mediated Allosteric Regulation. PLoS Computational Biology. San Francisco: PUBLIC LIBRARY SCIENCE, 2012, roč. 8, č. 6, s. "nestránkováno", 11 s. ISSN 1553-7358. Dostupné z: https://dx.doi.org/10.1371/journal.pcbi.1002565.

BERKA, Karel, Ondřej HANÁK, David SEHNAL, Pavel BANÁŠ, Veronika NAVRÁTILOVÁ, Deepti JAISWAL, Crina-Maria IONESCU, Radka SVOBODOVÁ VAŘEKOVÁ, Jaroslav KOČA a Michal OTYEPKA. MOLEonline 2.0: Interactive Web-based Analysis of Biomacromolecular Channels. Nucleic Acids Research. Oxford, UK: Oxford Press, 2012, roč. 40, W1, s. "W222"–"W227", 6 s. ISSN 0305-1048. Dostupné z: https://dx.doi.org/10.1093/nar/gks363.

GEIDL, Stanislav, Radka SVOBODOVÁ VAŘEKOVÁ, Crina-Maria IONESCU, Ondřej SKŘEHOTA, Tomáš BOUCHAL, Michal KUDERA, David SEHNAL, Abagyan RUBEN a Jaroslav KOČA. Predicting pKa values of substituted phenols by QSPR models which employ EEM atomic charges. In 3rd Strasbourg Summer School in Chemoinformatics. 2012.

IONESCU, Crina-Maria, Radka SVOBODOVÁ VAŘEKOVÁ a Jaroslav KOČA. Protein Politics: How Neutral is Neutral? In X Girona Seminar on Theoretical and Computational Chemistry for the Modeling of Biochemical Systems From Theory to Applications. 2012.

IONESCU, Crina-Maria, Radka SVOBODOVÁ VAŘEKOVÁ a Jaroslav KOČA. Quantum Mechanical Evaluation of Charge Transfer inside Proteins. In 3rd Strasbourg Summer School in Chemoinformatics. 2012.

IONESCU, Crina-Maria, Radka SVOBODOVÁ VAŘEKOVÁ, Heinrich J HUBER a Jaroslav KOČA. ROLE OF CHARGE TRANSFER IN THE ACTIVATION OF PRO-APOPTOTIC REGULATORS BAX AND BAK. In XXIII. biochemický sjezd České společnosti pro biochemii a molekulární biologii a Slovenské spoločnosti pre biochémiu a molekulárnu biológiu. 2012.

SEHNAL, David, Radka SVOBODOVÁ VAŘEKOVÁ, Heinrich J. HUBER, Stanislav GEIDL, Crina-Maria IONESCU, Michaela WIMMEROVÁ a Jaroslav KOČA. SiteBinder: An improved approach for comparing multiple protein structural motifs. Journal of Chemical Information and Modeling. 2012, roč. 52, č. 2, s. 343–359. ISSN 1549-9596. Dostupné z: https://dx.doi.org/10.1021/ci200444d.

SVOBODOVÁ VAŘEKOVÁ, Radka, David SEHNAL, Lukáš PRAVDA, Jan OPPELT, Crina-Maria IONESCU, Stanislav GEIDL a Jaroslav KOČA. Comparison of protein structural motifs – challenges and algorithms. Improved approach and case studies. In 9th International Conference on Chemical Structures, Noordwijkerhout, The Netherlands. 2011.

IONESCU, Crina-Maria, Radka SVOBODOVÁ VAŘEKOVÁ, David SEHNAL, Ondřej SKŘEHOTA a Jaroslav KOČA. Fast methods of atomic charge calculation: the Electronegativity Equalization Method for proteins. In 9th International Conference on Chemical Structures, Noordwijkerhout, The Netherlands. 2011.

GEIDL, Stanislav, Radka SVOBODOVÁ VAŘEKOVÁ, Ondřej SKŘEHOTA, Michal KUDERA, Crina-Maria IONESCU, David SEHNAL, Tomáš BOUCHAL a Jaroslav KOČA. Predicting pKa values of substituted phenols from atomic charges. In 9th Discussions in Structural Molecular Biology, Nové Hrady, Czech Republic. 2011.

SVOBODOVÁ VAŘEKOVÁ, Radka, Stanislav GEIDL, Crina-Maria IONESCU, Ondřej SKŘEHOTA, Michal KUDERA, David SEHNAL, Tomáš BOUCHAL, Ruben A. ABAGYAN, Heinrich J. HUBER a Jaroslav KOČA. Predicting pK(a) values of substituted phenols from atomic charges: Comparison of different quantum mechanical methods and charge distribution schemes. Journal of Chemical Information and Modeling. 2011, roč. 51, č. 8, s. 1795-1806. ISSN 1549-9596.

SKŘEHOTA, Ondřej, Radka SVOBODOVÁ VAŘEKOVÁ, Stanislav GEIDL, Crina-Maria IONESCU, Žídek JAN a Jaroslav KOČA. QSPR Designer – Employ your own descriptors in the automated QSAR modeling process. In 7th German Conference on Chemoinformatics. 2011.

SKŘEHOTA, Ondřej, Radka SVOBODOVÁ VAŘEKOVÁ, Stanislav GEIDL, Michal KUDERA, David SEHNAL, Crina-Maria IONESCU, Tomáš BOUCHAL a Jaroslav KOČA. QSPR modeling – algorithms, challenges and IT solutions. In 9th Discussions in Structural Molecular Biology, Nové Hrady, Czech Republic. 2011.

JAISWAL, Deepti, Radka SVOBODOVÁ VAŘEKOVÁ, Crina-Maria IONESCU, David SEHNAL a Jaroslav KOČA. Searching for tunnels of proteins - comparison of approaches and available software tools. In 7th German Conference on Chemoinformatics. 2011.

SEHNAL, David, Radka SVOBODOVÁ VAŘEKOVÁ, Heinrich J. HUBER, Stanislav GEIDL, Crina-Maria IONESCU, Michaela WIMMEROVÁ a Jaroslav KOČA. SiteBinder – an improved approach for comparing multiple protein structural motifs. Case studies on biologically important motifs. In 7th German Conference on Chemoinformatics. 2011.

SEHNAL, David, Radka SVOBODOVÁ VAŘEKOVÁ, Heinrich J. HUBER, Stanislav GEIDL, Crina-Maria IONESCU, Michaela WIMMEROVÁ a Jaroslav KOČA. SiteBinder – an improved software superimposing multiple protein structural motifs and its applications. In XV. Meeting of Biochemists and Molecular Biologists. 2011. ISBN 978-80-210-5594-0.

IONESCU, Crina-Maria, Radka SVOBODOVÁ VAŘEKOVÁ, Jakub VANĚK a Jaroslav KOČA. Fast methods of atomic charge calculation: parameterization of EEM for applicability to metal containing proteins. In 8th Discussions in Structural Molecular Biology. 2010.

IONESCU, Crina-Maria, Radka SVOBODOVÁ VAŘEKOVÁ, Tomáš RADĚJ, Ondřej SKŘEHOTA a Jaroslav KOČA. Fast methods of atomic charge calculation: parameterization of EEM for applicability to proteins. In 8th European Conference on Computational Chemistry. 2010.

SKŘEHOTA, Ondřej, Radka SVOBODOVÁ VAŘEKOVÁ, Stanislav GEIDL, Michal KUDERA, David SEHNAL, Crina-Maria IONESCU a Jaroslav KOČA. QSPR Designer - a program to design and evaluate QSPR models. Case study on pKa prediction. In 6th German Conference on Chemoinformatics. 2010.