Výpis publikací

SLANINÁKOVÁ, Terézia, David PROCHÁZKA, Jakub ČILLÍK, Lucie NOVOTNÁ a Adrián ROŠINEC. AlphaFind. 2024. Dostupné z: https://dx.doi.org/10.5281/zenodo.11085862.

SLANINÁKOVÁ, Terézia, David PROCHÁZKA, Jaroslav OĽHA, Adrián ROŠINEC, Katarína GREŠOVÁ, Jakub ČILLÍK, Miriama JÁNOŠOVÁ, Jana PORUBSKÁ, Radka SVOBODOVÁ, Vlastislav DOHNAL a Matej ANTOL. AlphaFind — discover structure similarity across the proteome in AlphaFold DB. In Elixir All-Hands 2024. 2024. Dostupné z: https://dx.doi.org/10.7490/f1000research.1119872.1.

GREŠOVÁ, Katarína, Pavlína ŠPRINGEROVÁ, Terézia SLANINÁKOVÁ, David PROCHÁZKA, Jaroslav OĽHA, Adrián ROŠINEC, Miriama JÁNOŠOVÁ, Jakub ČILLÍK, Jana PORUBSKÁ, Radka SVOBODOVÁ, Vlastislav DOHNAL a Matej ANTOL. AlphaFind — discover structure similarity across the proteome in AlphaFold DB. In ECCB2024. 2024.

PROCHÁZKA, David, Terézia SLANINÁKOVÁ, Jaroslav OĽHA, Adrián ROŠINEC, Katarína GREŠOVÁ, Miriama JÁNOŠOVÁ, Jakub ČILLÍK, Jana PORUBSKÁ, Radka SVOBODOVÁ, Vlastislav DOHNAL a Matej ANTOL. AlphaFind: Discover structure similarity across the entire known proteome. bioRxiv, 2024.

NOVOTNÁ, Lucie, Terézia SLANINÁKOVÁ, David PROCHÁZKA, Lukáš HEJTMÁNEK, Katarína GREŠOVÁ, Jaroslav OĽHA, Vlastislav DOHNAL, Adrián ROŠINEC a Matej ANTOL. AlphaFind: Discover structure similarity across the entire known proteome – data and model. 2024. Dostupné z: https://dx.doi.org/10.48700/datst.d35zf-1ja47.

PROCHÁZKA, David, Terézia SLANINÁKOVÁ, Jaroslav OĽHA, Adrián ROŠINEC, Katarína GREŠOVÁ, Miriama JÁNOŠOVÁ, Jakub ČILLÍK, Jana PORUBSKÁ, Radka SVOBODOVÁ, Vlastislav DOHNAL a Matej ANTOL. AlphaFind: discover structure similarity across the proteome in AlphaFold DB. Nucleic acids research. Oxford: Oxford University Press, 2024, roč. 52, July 5, s. W182-W186, 5 s. ISSN 0305-1048. Dostupné z: https://dx.doi.org/10.1093/nar/gkae397.

ROŠINEC, Adrián, Tomáš PAVLÍK, Terézia SLANINÁKOVÁ, Aleš KŘENEK, Pavlína ŠPRINGEROVÁ, Matej ANTOL a Radka SVOBODOVÁ. Beyond Metadata: Leveraging Similarity Search in Molecular Dynamics Data. In 2nd BioExcel Conference on Advances in Biomolecular Simulations. 2024. Dostupné z: https://dx.doi.org/10.5281/zenodo.14500696.

FALTINEK, Lukáš, Filip MELICHER, Viktor KELEMEN, Erika MEZŐ, Anikó BORBÁS a Michaela WIMMEROVÁ. Bispecific Thio-linked Disaccharides as Inhibitors of Pseudomonas aeruginosa Lectins LecA (PA-IL) and LecB (PA-IIL): Dual-Targeting Strategy. Chemistry – A European Journal. Wiley, 2024. ISSN 0947-6539. Dostupné z: https://dx.doi.org/10.1002/chem.202403546.

HOŠKOVÁ, Kateřina, Šárka FAJTLOVÁ, Pavel PLEVKA, Michal MIKL, Milan EŠNER, Radka SVOBODOVÁ a Boris TICHÝ. CF Day 2023. 2024.

SVOBODA, Tomáš, Jakub ČILLÍK, Michal MIKL, Tomáš SLAVÍČEK a Radka SVOBODOVÁ. Data Management and FAIRification in MAFIL. In Czech‐BioImaging Annual Scientific Conference 2024: Imaging Principles of Life. 2024.

SVOBODA, Tomáš, Adrián ROŠINEC, Tomáš RAČEK a Radka SVOBODOVÁ. Data Management of Biological Imaging Data. In ELIXIR CZ Annual Conference 2024: Data management. 2024.

SVOBODA, Tomáš a Adrián ROŠINEC. Data workflows at CEITEC MU. In Setkání OS metodiků MU. 2024.

SLANINÁKOVÁ, Terézia, Katarína GREŠOVÁ, David PROCHÁZKA, Viktória SPIŠAKOVÁ, Adrián ROŠINEC, Jakub ČILLÍK, Pavlína ŠPRINGEROVÁ, Aleš KŘENEK, Vlastislav DOHNAL, Radka SVOBODOVÁ a Matej ANTOL. Fast, structure-based searching in a large-scale protein data repository. In ELIXIR CZ Annual Conference. 2024. Dostupné z: https://dx.doi.org/10.13140/RG.2.2.31355.53281.

NOVOTNÁ, Lucie, Terézia SLANINÁKOVÁ, David PROCHÁZKA, Lukáš HEJTMÁNEK, Adrián ROŠINEC, Jaroslav OĽHA, Katarína GREŠOVÁ, Vlastislav DOHNAL a Matej ANTOL. GraSR: Protein structural embeddings of AlphaFold DB. 2024. Dostupné z: https://dx.doi.org/10.48700/datst.br8aq-db495.

SVOBODA, Tomáš, Adrián ROŠINEC a Ondřej FILIP. Hands-on experience with big data transfer via iRODS and Onedata. In e-INFRA CZ CONFERENCE 2024. 2024.

ŠPAČKOVÁ, Anna, Ondřej VÁVRA, Tomáš RAČEK, Václav BAZGIER, David SEHNAL, Jiří DAMBORSKÝ, Radka SVOBODOVÁ, David BEDNÁŘ a Karel BERKA. ChannelsDB 2.0: a comprehensive database of protein tunnels and pores in AlphaFold era. Nucleic Acids Research. Oxford University Press, 2024, roč. 52, D1, s. "D413"-"D418", 6 s. ISSN 0305-1048. Dostupné z: https://dx.doi.org/10.1093/nar/gkad1012.

ROŠINEC, Adrián. Introduction to the new generation EGI container execution platform. In EGI Webinar programme 2024. 2024. Dostupné z: https://dx.doi.org/10.5281/zenodo.10566759.

NOVOTNÁ, Lucie, Terézia SLANINÁKOVÁ, David PROCHÁZKA, Lukáš HEJTMÁNEK, Adrián ROŠINEC, Jaroslav OĽHA, Katarína GREŠOVÁ, Vlastislav DOHNAL a Matej ANTOL. LMI-10: Protein structural embeddings of AlphaFold DB. 2024. Dostupné z: https://dx.doi.org/10.48700/datst.t45hr-bcw17.

NOVOTNÁ, Lucie, Terézia SLANINÁKOVÁ, David PROCHÁZKA, Lukáš HEJTMÁNEK, Adrián ROŠINEC, Jaroslav OĽHA, Katarína GREŠOVÁ, Vlastislav DOHNAL a Matej ANTOL. LMI-30: Protein structural embeddings of AlphaFold DB. 2024. Dostupné z: https://dx.doi.org/10.48700/datst.kgb8j-r5f84.

SVOBODA, Tomáš. MAFILDB - technická realizace. In FAIR data pro uživatele CF MAFIL. 2024.

BUČEKOVÁ, Gabriela, Viktoriia DOSHCHENKO, Aliaksei CHARESHNEU, Jana PORUBSKÁ, Michal PAJTINKA, Michal OLEKSIK, Tomáš SVOBODA, Vladimír HORSKÝ a Radka SVOBODOVÁ. Rare ring conformations in PDB: Facts or wishful thinking? bioRxiv. 2024. Dostupné z: https://dx.doi.org/10.1101/2024.06.20.598822.

GREŠOVÁ, Katarína, Tomáš RAČEK, Vlastimil MARTINEK, David ČECHÁK, Radka SVOBODOVÁ a Panagiotis ALEXIOU. RBP-Tar – a searchable database for experimental RBP binding sites. F1000Research. 2024. Dostupné z: https://dx.doi.org/10.12688/f1000research.131014.2.

ROŠINEC, Adrián a Tomáš SVOBODA. Research Data Management at CEITEC MU. In Open Science Workshop 2024. 2024.

SVOBODA, Tomáš, Adrián ROŠINEC, Tomáš RAČEK, Josef HANDL, Aleš KŘENEK a Radka SVOBODOVÁ. Scientific Dataset Management System for the Research Institute Based on Onedata. In EGI Conference 2024. 2024.

NOVOTNÁ, Lucie, Terézia SLANINÁKOVÁ, David PROCHÁZKA, Lukáš HEJTMÁNEK, Adrián ROŠINEC, Jaroslav OĽHA, Katarína GREŠOVÁ, Vlastislav DOHNAL a Matej ANTOL. 3D-af-Surfer: Protein structural embeddings of AlphaFold DB. 2024. Dostupné z: https://dx.doi.org/10.48700/datst.tbws0-hj147.

CALATRAVA, Amanda, Hernán ASOREY, Jan ASTALOS, Alberto AZEVEDO, Francesco BENINCASA, Ignacio BLANQUER, Martin BOBAK, Francisco BRASILEIRO, Laia CODÓ, Laura del CANO, Borja ESTEBAN, Meritxell FERRET, Josef HANDL, Tobias KERZENMACHER, Valentin KOZLOV, Aleš KŘENEK, Ricardo MARTINS, Manuel PAVESIO, Antonio Juan RUBIO-MONTERO a Juan SÁNCHEZ-FERRERO. A survey of the European Open Science Cloud services for expanding the capacity and capabilities of multidisciplinary scientific applications. COMPUTER SCIENCE REVIEW. NETHERLANDS: ELSEVIER, 2023, roč. 49. ISSN 1574-0137. Dostupné z: https://dx.doi.org/10.1016/j.cosrev.2023.100571.

LAMOTHE, Lucie, Jennifer R B JENSEN, Hans IENASESCU, Ove J R GUSTAFSSON, Alban GAIGNARD, Dmitry REPCHEVSKY, Radka SVOBODOVÁ, Tomáš RAČEK, Adrián ROŠINEC, Matej ANTOL a Hervé MÉNAGER. An Evaluation of EDAM Coverage in the Tools Ecosystem and Prototype Integration of Galaxy and Workflowhub Systems. BioHackrXiv. 2023, s. 1-10. Dostupné z: https://dx.doi.org/10.37044/osf.io/79kje.

APPASAMY, Sri Devan, John BERRISFORD, Romana GÁBOROVÁ, Sreenath NAIR, Stephen ANYANGO, Sergei GRUDININ, Mandar DESHPANDE, David ARMSTRONG, Ivanna PIDRUCHNA, Joseph I. J. ELLAWAY, Grisell Díaz LEINES, Deepti GUPTA, Deborah HARRUS, Mihaly VARADI a Sameer VELANKAR. Annotating Macromolecular Complexes in the Protein Data Bank: Improving the FAIRness of Structure Data. Scientific Data. Nature Portfolio, 2023, roč. 10, č. 1, s. 1-13. ISSN 2052-4463. Dostupné z: https://dx.doi.org/10.1038/s41597-023-02778-9.

ROŠINEC, Adrián a Klára MORAVCOVÁ. Beskar Cloud: OpenStack Deployment on Top of Kubernetes. In 12th Iberian Grid Conference. 2023.

ROŠINEC, Adrián a Klára MORAVCOVÁ. Building OpenStack Cloud with Kubernetes as Undercloud. In EGI Conference 2023. 2023.

SVOBODA, Tomáš, Aleš KŘENEK, Łukasz OPIOŁA, Andrea MANZI a Josef HANDL. Cloudification of scientific experimental data using Onedata. In EGI Conference 2023. 2023.

BUČEKOVÁ, Gabriela, Viktoriia DOSHCHENKO, Vladimír HORSKÝ a Radka SVOBODOVÁ. Conformational study of small carbon rings in ligands. In 3D-BioInfo | ICSB 3D-SIG | ELIXIR Czech Republic Community Meeting in Structural Bioinformatics. 2023.

HEJTMÁNEK, Lukáš, Adrián ROŠINEC a Sebastian LUNA-VALERO. Easy Deployment of Dask and Jupyter Notebooks on Managed Kubernetes. In EGI Conference 2023. 2023.

TURNER, Jack, Sanja ABBOTT, Neli FONSECA, Lucas CARRIJO, Amudha Kumari DURAISAMY, Osman SALIH, Zhe WANG, Gerard J KLEYWEGT, Kyle L MORRIS, Ardan PATWARDHAN, Stephen K BURLEY, Gregg CRICHLOW, Zukang FENG, Justin W FLATT, Sutapa GHOSH, Brian P HUDSON, Catherine L LAWSON, Yuhe LIANG, Ezra PEISACH, Irina PERSIKOVA, Monica SEKHARAN, Chenghua SHAO, Jasmine YOUNG, Sameer VELANKAR, David ARMSTRONG, Marcus BAGE, Wesley Morellato BUENO, Genevieve EVANS, Romana GÁBOROVÁ, Sudakshina GANGULY, Deepti GUPTA, Deborah HARRUS, Ahsan TANWEER, Manju BANSAL, Vetriselvi RANGANNAN, Genji KURISU, Hasumi CHO, Yasuyo IKEGAWA, Yumiko KENGAKU, Ju Yaen KIM, Satomi NIWA, Junko SATO, Ayako TAKUWA, Jian YU, Jeffrey C HOCH, Kumaran BASKARAN, Wenqing XU, Weizhe ZHANG a Xiaodan MA. EMDB-the Electron Microscopy Data Bank. Nucleic acids research. Oxford: Oxford University Press, 2023, roč. 52, Jan, s. 456-465. ISSN 0305-1048. Dostupné z: https://dx.doi.org/10.1093/nar/gkad1019.

ROŠINEC, Adrián, Tomáš SVOBODA, Tomáš RAČEK, Aleš KŘENEK a Radka SVOBODOVÁ. Enhancing Data Accessibility: Strategies and Tools for Effective Metadata Management. In IBERGRID 2023. 2023.

PORUBSKÁ, Jana, Veronika HORSKÁ, Vladimír HORSKÝ a Radka SVOBODOVÁ. Exploring the relationship between structural quality and journal impact factor. In 3D-BioInfo | ICSB 3D-SIG | ELIXIR Czech Republic Community Meeting in Structural Bioinformatics. 2023.

ŠPAČKOVÁ, Anna, Ondřej VÁVRA, Tomáš RAČEK, Václav BAZGIER, David SEHNAL, Jiří DAMBORSKÝ, Radka SVOBODOVÁ a Karel BERKA. ChannelsDB 2.0: A Comprehensive Database of Protein Tunnels and Pores in AlphaFold Era. In 3D-BioInfo | ICSB 3D-SIG | ELIXIR Czech Republic Community Meeting in Structural Bioinformatics. 2023.

SCHINDLER, Ondřej, Karel BERKA, Alessio CANTARA, Aleš KŘENEK, Dominik TICHÝ, Tomáš RAČEK a Radka SVOBODOVÁ. αCharges: partial atomic charges for AlphaFold structures in high quality. Nucleic Acids Research. Oxford: Oxford University Press, 2023, roč. 51, W1, s. "W11"-"W16", 6 s. ISSN 0305-1048. Dostupné z: https://dx.doi.org/10.1093/nar/gkad349.

SVOBODA, Tomáš, Radka SVOBODOVÁ, David ANTOŠ, Adrián ROŠINEC a Aleš KŘENEK. Introduction to Onedata at CEITEC MU and in Czech National Repository Platform. In MATECHat meeting. 2023.

BUČEKOVÁ, Gabriela, Viktoriia DOSHCHENKO, Vladimír HORSKÝ a Radka SVOBODOVÁ. Invesigating the rare conformation of small rings in ligands. In XXII. Meeting of Biochemists and Molecular Biologists. 2023.

PORUBSKÁ, Jana, Veronika HORSKÁ, Vladimír HORSKÝ a Radka SVOBODOVÁ. Journal metrics and structures: A dynamic interplay. In XXII. Meeting of Biochemists and Molecular Biologists. 2023. ISBN 978-80-280-0409-5.

RAČEK, Tomáš, Tomáš SVOBODA a Radka SVOBODOVÁ. Management of life-science data and their metadata. In XXII. setkání biochemiků a molekulárních biologů. 2023.

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.

SVOBODOVÁ, Radka, Karel BERKA, Ivana HUTAŘOVÁ VAŘEKOVÁ, Tomáš RAČEK a Ondřej SCHINDLER. New ways of protein family visualization in AlphaFold era. In 3D-BioInfo | ICSB 3D-SIG | ELIXIR Czech Republic Community Meeting in Structural Bioinformatics. 2023.

ROŠINEC, Adrián, Tomáš SVOBODA, Tomáš RAČEK, Josef HANDL, Jozef SABO, Aleš KŘENEK a Radka SVOBODOVÁ. Onedata4Sci: Life-science experimental datasets management system. In 3D-BioInfo | ISCB 3D-SIG | ELIXIR Czech Republic Structural Bioinformatics. 2023.

RAČEK, Tomáš. Zpracování dat na CEITECu. In SitSem - Seminář laboratoře Sitola. 2023.

KIVINEN, Katja, Henri VAN LUENEN, Myriam ALCALAY, Christoph BOCK, Joanna DODZIAN, Kateřina HOŠKOVÁ, Danielle HOYLE, Ondřej HRADIL, Sofie Kjellerup CHRISTENSEN, Bernhard KORN, Theodoros KOSTEAS, Monica MORALES, Krzysztof SKOWRONEK, Vasiliki THEODOROU, Van Minnebruggen GEERT, Jean SALAMERO a Lavanya PREMVARDHAN. Acknowledging and citing core facilities Key contributions to data lifecycle should be recognised in the scientific literature. EMBO reports. Hoboken: Wiley-Blackwell, 2022, roč. 23, č. 9, s. 1-3. ISSN 1469-221X. Dostupné z: https://dx.doi.org/10.15252/embr.202255734.

SCHINDLER, Ondřej, Tomáš RAČEK a Radka SVOBODOVÁ. Alphacharges - a web service for calculating QM-like partial atomic charges for AlphaFold proteins. In XXI. setkání biochemiků a molekulárních biologů. 2022.

RAČEK, Tomáš, Ondřej SCHINDLER, Lenka PTÁČNÍKOVÁ a Radka SVOBODOVÁ. Atomic Charge Calculator II – a web service for calculating partial atomic charges. In ENBIK2022. 2022. ISBN 978-80-7592-127-7.

SVOBODA, Tomáš, Aleš KŘENEK a Josef HANDL. Automatic storing, sharing and archiving datasets with Onedata. In EGI Conference 2022. 2022.

SVOBODA, Tomáš, Aleš KŘENEK a Josef HANDL. Automating scientific dataset management and processing using Onedata. In IBERGRID 2022. 2022.

SKLENÁŘ, Vladimír, Radovan FIALA, Jiří NOVÁČEK, Josef HOUSER, Jan PŘIBYL, Zbyněk ZDRÁHAL, Milan EŠNER, Michal MIKL, Boris TICHÝ, Vojtěch BYSTRÝ a Radka SVOBODOVÁ. CF Day Meeting. 2022.

CHARESHNEU, Aliaksei, David SEHNAL a Radka SVOBODOVÁ. CoverView: clear atom-level visualization of electron density coverage of PDB structures to assist validation. 2022.

HRADIL, Ondřej, Václav TESAŘ a Zuzana VÉMOLOVÁ. International Conference on Research Infrastructures 2022. Proceedings Report. 1., elektronické vyd. Brno: Masarykova univerzita, 2022. ISBN 978-80-280-0148-3.

MIDLIK, Adam, Ivana HUTAŘOVÁ VAŘEKOVÁ, Jan HUTAŘ, Aliaksei CHARESHNEU, Karel BERKA a Radka SVOBODOVÁ. OverProt: secondary structure consensus for protein families. Bioinformatics. Oxford University Press, 2022, roč. 38, č. 14, s. 3648-3650. ISSN 1367-4803. Dostupné z: https://dx.doi.org/10.1093/bioinformatics/btac384.

VARADI, Mihaly, Stephen ANYANGO, Sri Devan APPASAMY, David ARMSTRONG, Marcus BAGE, John BERRISFORD, Preeti CHOUDHARY, Damian BERTONI, Mandar DESHPANDE, Grisell Diaz LEINES, Joseph ELLAWAY, Genevieve EVANS, Romana GÁBOROVÁ, Deepti GUPTA, Aleksandras GUTMANAS, Deborah HARRUS, Gerard J KLEYWEGT, Weslley Morellato BUENO, Nurul NADZIRIN, Sreenath NAIR, Lukas PRAVDA, Marcelo Querino Lima AFONSO, David SEHNAL, Ahsan TANWEER, James TOLCHARD, Charlotte ABRAMS, Roisin DUNLOP a Sameer VELANKAR. PDBe and PDBe-KB: Providing high-quality, up-to-date and integrated resources of macromolecular structures to support basic and applied research and education. Protein Science. Wiley, 2022, roč. 31, č. 10, s. 1-10. ISSN 0961-8368. Dostupné z: https://dx.doi.org/10.1002/pro.4439.

VARADI, Mihaly, Stephen ANYANGO, Sri Devan APPASAMY, David ARMSTRONG, Marcus BAGE, John BERRISFORD, Preeti CHOUDHARY, Damian BERTONI, Mandar DESHPANDE, Grisell Diaz LEINES, Joseph ELLAWAY, Genevieve EVANS, Romana GABOROVA, Deepti GUPTA, Aleksandras GUTMANAS, Deborah HARRUS, Gerard J KLEYWEGT, Weslley Morellato BUENO, Nurul NADZIRIN, Sreenath NAIR, Lukas PRAVDA, Marcelo Querino Lima AFONSO, David SEHNAL, Ahsan TANWEER, James TOLCHARD, Charlotte ABRAMS, Roisin DUNLOP a Sameer VELANKAR. PDBe and PDBe-KB: Providing high-quality, up-to-date and integrated resources of macromolecular structures to support basic and applied research and education. Protein Science. HOBOKEN: WILEY, 2022, roč. 31, č. 10, 10 s. ISSN 0961-8368. Dostupné z: https://dx.doi.org/10.1002/pro.4439.

VARADI, Mihaly, Stephen ANYANGO, David ARMSTRONG, John BERRISFORD, Preeti CHOUDHARY, Mandar DESHPANDE, Nurul NADZIRIN, Sreenatha S. NAIR, Lukas PRAVDA, Ahsan TANWEER, Bissan AL-LAZIKANI, Claudia ANDREINI, Geoffrey J. BARTON, David BEDNÁŘ, Karel BERKA, Tom BLUNDELL, Kelly P. BROCK, Jose MARIA CARAZO, Jiří DAMBORSKÝ, Alessia DAVID, Sucharita DEY, Roland DUNBRACK, Fernandez Juan RECIO, Franca FRATERNALI, Toby GIBSON, Manuela HELMER-CITTERICH, David HOKSZA, Thomas HOPF, David JAKUBEC, Natarajan KANNAN, Radoslav KRIVAK, Manjeet KUMAR, Emmanuel D. LEVY, Nir LONDON, Jose Ramon MACIAS, Madhusudhan M. SRIVATSAN, Debora S. MARKS, Lennart MARTENS, Stuart A. MCGOWAN, Jake E. MCGREIG, Vivek MODI, Gonzalo R. PARRA, Gerardo PEPE, Damiano PIOVESAN, Jaime PRILUSKY, Valeria PUTIGNANO, Leandro G. RADUSKY, Pathmanaban RAMASAMY, Atilio O. RAUSCH, Nathalie REUTER, Luis A. RODRIGUEZ, Nathan J. ROLLINS, Antonio ROSATO, Luis SERRANO, Gulzar SINGH, Petr SKODA, Carlos Oscar S. SORZANO, Jan ŠTOURAČ, Joanna I. SULKOWSKA, Radka SVOBODOVÁ, Natalia TICHSHENKO, Silvio C. E. TOSATTO, Wim VRANKEN, Mark N. WASS, Dandan XUE, Daniel ZAIDMAN, Janet THORNTON, Michael STERNBERG, Christine ORENGO a Sameer VELANKAR. PDBe-KB: collaboratively defining the biological context of structural data. Nucleic acids research. Oxford: Oxford University Press, 2022, roč. 50, D1, s. "D534"-"D542", 9 s. ISSN 0305-1048. Dostupné z: https://dx.doi.org/10.1093/nar/gkab988.

SCHINDLER, Ondřej, Tomáš RAČEK a Radka SVOBODOVÁ. Prediction of QM-like partial atomic charges for alphafold. In XXII. Workshop of biophysical chemists and electrochemists. 2022. ISBN 978-80-280-0087-5.

SCHINDLER, Ondřej, Tomáš RAČEK, Kamil JELÍNEK a Radka SVOBODOVÁ. QM-like partial atomic charges for AlphaFold available online. In ENBIK2022. 2022. ISBN 978-80-7592-127-7.

DUDOVÁ, Zdenka, Nathalie CONTE, Jeremy MASON, Dalibor STUCHLÍK, Radim PEŠA, Csaba HALMAGYI, Zinaida PEROVA, Abayomi MOSAKU, Ross THORNE, Alex FOLLETTE, Ľuboslav PIVARČ, Radim ŠAŠINKA, Muhammad USMAN, Steven NEUHAUSER, Dale A BEGLEY, Debra M KRUPKE, Massimiliano FRASSÀ, Alessandro FIORI, Riccardo CORSI, Luca VEZZADINI, Claudio ISELLA, Andrea BERTOTTI, Carol BULT, Helen PARKINSON, Enzo MEDICO, Terrence MEEHAN a Aleš KŘENEK. The EurOPDX Data Portal: an open platform for patient-derived cancer xenograft data sharing and visualization. BMC Genomics. BioMed Central, 2022, roč. 23, č. 1, s. 1-11. ISSN 1471-2164. Dostupné z: https://dx.doi.org/10.1186/s12864-022-08367-1.

BUČEKOVÁ, Gabriela, Viktoriia DOSHCHENKO, Aliaksei CHARESHNEU a Radka SVOBODOVÁ. Validation of cycle conformation in small molecules. In XXI. Meeting of Biochemists and Molecular Biologists. 2022.

SILLITOE, Ian, Nicola BORDIN, Natalie DAWSON, Vaishali P. WAMAN, Paul ASHFORD, Harry M. SCHOLES, Camilla S.M. PANG, Laurel WOODRIDGE, Clemens RAUER, Neeladri SEN, Mahnaz ABBASIAN, Sean LE CORNU, Su Datt LAM, Karel BERKA, Ivana HUTAŘOVÁ VAŘEKOVÁ, Radka SVOBODOVÁ, Jon LEES a Christine A. ORENGO. CATH: increased structural coverage of functional space. Nucleic Acids Research. Oxford: Oxford University Press, 2021, roč. 49, D1, s. "D266"-"D273", 8 s. ISSN 0305-1048. Dostupné z: https://dx.doi.org/10.1093/nar/gkaa1079.

RAČEK, Tomáš a Ondřej SCHINDLER. COMPUTER-AIDED MODEL DESIGN OF EMPIRICAL METHODS FOR CALCULATING PARTIAL ATOMIC CHARGES. Online. In 978-9-492-85918-1. MODELLING AND SIMULATION 2021: 35TH ANNUAL EUROPEAN SIMULATION AND MODELLING CONFERENCE 2021 (ESM 2021). GHENT: EUROSIS, 2021, s. 16-20. ISBN 978-94-92859-18-1.

SEHNAL, David, S. BITTRICH, M. DESHPANDE, Radka SVOBODOVÁ, K. BERKA, V. BAZGIER, S. VELANKAR, S.K. BURLEY, Jaroslav KOČA a A.S. ROSE. Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures. Nucleic acids research. Oxford: Oxford University Press, 2021, roč. 49, W1, s. "W431"-"W437", 7 s. ISSN 0305-1048. Dostupné z: https://dx.doi.org/10.1093/nar/gkab314.

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HORSKÝ, Vladimír, Veronika BENDOVÁ, Radka SVOBODOVÁ VAŘEKOVÁ a Jaroslav KOČA. Exploring Trends in Quality of Biomacromolecular Structure Data. In ELIXIR CZ Annual Conference 2017. 2017. ISBN 978-80-86241-57-9.

JIMÉNEZ, Rafael C, Mateusz KUZAK, Monther ALHAMDOOSH, Michelle BARKER, Bérénice BATUT, Mikael BORG, Salvador CAPELLA-GUTIERREZ, Neil Chue HONG, Martin COOK, Manuel CORPAS, Madison FLANNERY, Leyla GARCIA, Josep Ll GELPÍ, Simon GLADMAN, Carole GOBLE, Montserrat González FERREIRO, Alejandra GONZALEZ-BELTRAN, Philippa C GRIFFIN, Björn GRÜNING, Jonas HAGBERG, Petr HOLUB, Rob HOOFT, Jon ISON, Daniel S KATZ, Brane LESKOŠEK, Federico López GÓMEZ, Luis J OLIVEIRA, David MELLOR, Rowland MOSBERGEN, Nicola MULDER, Yasset PEREZ-RIVEROL, Robert PERGL, Horst PICHLER, Bernard POPE, Ferran SANZ, Maria V SCHNEIDER, Victoria STODDEN, Radosław SUCHECKI, Radka SVOBODOVÁ VAŘEKOVÁ, Harry-Anton TALVIK, Ilian TODOROV, Andrew TRELOAR, Sonika TYAGI, Maarten van GOMPEL, Daniel VAUGHAN, Allegra VIA, Xiaochuan WANG, Nathan S WATSON-HAIGH a Crouch STEVE. Four simple recommendations to encourage best practices in research software. F1000Research. 2017, roč. 6, JUN, s. 876-888. ISSN 2046-1402. Dostupné z: https://dx.doi.org/10.12688/f1000research.11407.1.

SEHNAL, David, Mandar DESHPANDE, Radka SVOBODOVÁ VAŘEKOVÁ, Saqib MIR, Karel BERKA, Adam MIDLIK, Lukáš PRAVDA, Sameer VELANKAR a Jaroslav KOČA. LiteMol suite: interactive web-based visualization of large-scale macromolecular structure data. Nature Methods. London, United Kingdom: Nature Publishing Group, 2017, roč. 14, č. 12, s. 1121-1122. ISSN 1548-7091. Dostupné z: https://dx.doi.org/10.1038/nmeth.4499.

HUTAŘOVÁ VAŘEKOVÁ, Ivana, Jan HUTAŘ, Radka SVOBODOVÁ VAŘEKOVÁ a Karel BERKA. Mapping and 2D visualization of secondary structure elements in cytochromes. In ISMB/ECCB, Prague. 2017.

SVOBODOVÁ VAŘEKOVÁ, Radka, Vladimír HORSKÝ, David SEHNAL, Veronika BENDOVÁ, Lukáš PRAVDA a Jaroslav KOČA. Quo Vadis, Biomacromolecular Structure Quality. In Biophysical Society 61st Annual Meeting, New Orleans, Louisiana. 2017. ISSN 1542-0086. Dostupné z: https://dx.doi.org/10.1016/j.bpj.2016.11.1880.

HORSKÝ, Vladimír, Veronika BENDOVÁ, Radka SVOBODOVÁ VAŘEKOVÁ a Jaroslav KOČA. Trends in biomacromolecular structure quality. In 2nd Annual Users Meeting of iNEXT. 2017.

HORSKÝ, Vladimír, Veronika BENDOVÁ, Radka SVOBODOVÁ VAŘEKOVÁ a Jaroslav KOČA. Trends in quality and properties of biomacromolecular complexes. In Curie - Pasteur - CEITEC joint young scientist retreat. 2017.

ŽUFANOVÁ, Zuzana, Radka SVOBODOVÁ VAŘEKOVÁ a Michaela WIMMEROVÁ. Validation and analyses of biomacromolecular ligand conformations. In CEITEC PhD Retreat II. 2017. ISBN 978-80-210-8550-3.

MIDLIK, Adam, Karel BERKA, Radka SVOBODOVÁ VAŘEKOVÁ a Jaroslav KOČA. Automatická anotácia sekundárnych štruktúr v cytochrómoch P450 a hodnotenie ich štruktúrnej podobnosti. In Národní bioinformatická konference ENBIK. 2016.

PRAVDA, Lukáš, David SEHNAL, Radka SVOBODOVÁ VAŘEKOVÁ a Jaroslav KOČA. Detekce biomolekulárních substruktur pomocí PatternQuery. In ENBIK - Národní bioinformatická konference. 2016. ISBN 978-80-7080-960-0.

HEJRET, Václav, Stanislav GEIDL, Radka SVOBODOVÁ VAŘEKOVÁ a Jaroslav KOČA. ChrgDescCalc.py – nástroj na výpočet nábojových deskriptorů. In ENBIK - Národní bioinformatická konference. 2016. ISBN 978-80-7080-960-0.

RAČEK, Tomáš, Radka SVOBODOVÁ VAŘEKOVÁ, Aleš KŘENEK, Jana PAZÚRIKOVÁ, Stanislav GEIDL a Jaroslav KOČA. NEEMP – nástroj pro parametrizaci EEM. In ENBIK2016. 2016. ISBN 978-80-7080-960-0.

RAČEK, Tomáš, Jana PAZÚRIKOVÁ, Radka SVOBODOVÁ VAŘEKOVÁ, Stanislav GEIDL, Aleš KŘENEK, Francesco Luca FALGINELLA, Vladimír HORSKÝ, Václav HEJRET a Jaroslav KOČA. NEEMP: software for validation, accurate calculation and fast parameterization of EEM charges. Journal of Cheminformatics. London: BIOMED CENTRAL LTD, 2016, roč. 8, October, s. nestránkováno, 14 s. ISSN 1758-2946. Dostupné z: https://dx.doi.org/10.1186/s13321-016-0171-1.

ADAMS, Paul D., Kathleen AERTGEERTS, Cary BAUER, Jeffrey A. BELL, Helen M. BERMAN, Talapady N. BHAT, Jeff M. BLANEY, Evan BOLTON, Gerard BRICOGNE, David BROWN, Stephen K. BURLEY, David A. CASE, Kirk L. CLARK, Tom DARDEN, Paul EMSLEY, Victoria A. FEHER, Zukang FENG, Colin R. GROOM, Seth F. HARRIS, Jorg HENDLE, Thomas HOLDER, Andrzej JOACHIMIAK, Gerard J. KLEYWEGT, Tobias KROJER, Joseph MARCOTRIGIANO, Alan E. MARK, John L. MARKLEY, Matthew MILLER, Wladek MINOR, Gaetano T. MONTELIONE, Garib MURSHUDOV, Atsushi NAKAGAWA, Haruki NAKAMURA, Anthony NICHOLLS, Marc NICKLAUS, Robet T. NOLTE, Anil K. PADYANA, Catherine E. PEISHOFF, Susan PIENIAZEK, Randy J. READ, Chenghua SHAO, Steven SHERIFF, Oliver SMART, Stephen SOISSON, John SPURLINO, Terry STOUCH, Radka SVOBODOVÁ VAŘEKOVÁ, Wolfram TEMPEL, Thomas C. TERWILLIGER, Dale TRONRUD, Sameer VELANKAR, Suzanna C. WARD, Gregory L. WARREN, John D. WESTBROOK, Pamela WILLIAMS, Huanwang YANG a Jasmine YOUNG. Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop. Structure. CAMBRIDGE: CELL PRESS, 2016, roč. 24, č. 4, s. 502-508. ISSN 0969-2126. Dostupné z: https://dx.doi.org/10.1016/j.str.2016.02.017.

PAZÚRIKOVÁ, Jana, Tomáš RAČEK, Stanislav GEIDL, Radka SVOBODOVÁ VAŘEKOVÁ a Aleš KŘENEK. Parametrizace ekvalizace elektronegativity metodou diferenciální evoluce. In ENBIK 2016. 2016.

KOČA, Jaroslav, Radka SVOBODOVÁ VAŘEKOVÁ, Lukáš PRAVDA, Karel BERKA, Stanislav GEIDL, David SEHNAL a Michal OTYEPKA. Structural Bioinformatics Tools for Drug Design: Extraction of Biologically Relevant Information from Structural Databases. Online. 1. vyd. Cham: Springer International Publishing, 2016, 144 s. SpringerBriefs in Biochemistry and Molecular Biology. ISBN 978-3-319-47388-8. Dostupné z: https://dx.doi.org/10.1007/978-3-319-47388-8.

PERCZEL, András, Atanas G. ATANASOV, Vladimír SKLENÁŘ, Jiří NOVÁČEK, Veronika PAPOUŠKOVÁ, Pavel KADEŘÁVEK, Lukáš ŽÍDEK, Henryk KOZLOWSKI, Joanna WATLY, Aleksandra HECEL, Paulina KOLKOWSKA, Jaroslav KOČA, Radka SVOBODOVÁ VAŘEKOVÁ, Lukáš PRAVDA, David SEHNAL, Vladimír HORSKÝ, Stanislav GEIDL, Ricardo D. ENRIZ, Pavel MATĚJKA, Adéla JENIŠTOVÁ, Marcela DENDISOVÁ, Alžběta KOKAISLOVÁ, Volkmar WEISSIG, Mark OLSEN, Aidan COFFEY, Jude AJUEBOR, Ruth KEARY, Marta SANZ-GAITERO, Mark J. VAN RAAIJ, Olivia MCAULIFFE, Birgit WALTENBERGER, Andrei MOCAN, Karel ŠMEJKAL, Elke H. HEISS, Marc DIEDERICH, Robert MUSIOL, Janez KOŠMRLJ, Jaroslaw POLANSKI a Josef JAMPÍLEK. The Eighth Central European Conference “Chemistry towards Biology”: Snapshot. MOLECULES. Basel: MDPI AG, 2016, roč. 21, č. 10, s. nestránkováno, 27 s. ISSN 1420-3049. Dostupné z: https://dx.doi.org/10.3390/molecules21101381.

ISON, Jon, Kristoffer RAPACKI, Herve MENAGER, Matus KALAS, Emil RYDZA, Piotr CHMURA, Christian ANTHON, Niall BEARD, Karel BERKA, Dan BOLSER, Tim BOOTH, Anthony BRETAUDEAU, Jan BREZOVSKÝ, 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, Bjoern GRUNING, Manuela HELMER-CITTERICH, Hans IENASESCU, Vassilios IOANNIDIS, Martin Closter JESPERSEN, Rafael JIMENEZ, Nick JUTY, Peter JUVAN, Maximilian KOCH, Camille LAIBE, Jing-Woei LI, Luana LICATA, Fabien MAREUIL, Ivan MICETIC, Rune Mollegaard FRIBORG, Sebastien MORETTI, Chris MORRIS, Steffen MOLLER, Aleksandra NENADIC, Hedi PETERSON, Giuseppe PROFITI, Peter RICE, Paolo ROMANO, Paola RONCAGLIA, Rabie SAIDI, Andrea SCHAFFERHANS, Veit SCHWAMMLE, Callum SMITH, Maria Maddalena SPEROTTO, Heinz STOCKINGER, Radka SVOBODOVÁ VAŘEKOVÁ, Silvio C. E. TOSATTO, Victor DE LA TORRE, Paolo UVA, Allegra VIA, Guy YACHDAV, Federico ZAMBELLI, Gert VRIEND, Burkhard ROST, Helen PARKINSON, Peter LONGREEN a Soren BRUNAK. Tools and data services registry: a community effort to document bioinformatics resources. Nucleic Acids Research. Oxford: Oxford University Press, 2016, roč. 44, D1, s. "D38"-"D47", 10 s. ISSN 0305-1048. Dostupné z: https://dx.doi.org/10.1093/nar/gkv1116.

ARTAZA, H., N. C. HONG, M. CORPAS, A. CORPUZ, R. HOOFT, R. C. JIMENEZ, B. LESKOŠEK, B. G. OLIVIER, J. STOURAC, Radka SVOBODOVÁ VAŘEKOVÁ, T. VAN PARYS a D. VAUGHAN. Top 10 metrics for life science software good practices [version 1; referees: 2 approved]. F1000Research. F1000 Research Ltd., 2016, roč. 5, August, s. nestránkováno, 9 s. ISSN 2046-1402. Dostupné z: https://dx.doi.org/10.12688/f1000research.9206.1.

GEIDL, Stanislav, Václav HEJRET, Radka SVOBODOVÁ VAŘEKOVÁ a Jaroslav KOČA. Využití nábojových deskriptorů v chemoinformatice. In ENBIK - Národní bioinformatická konference. 2016. ISBN 978-80-7080-960-0.

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, Tomáš BOUCHAL, Tomáš RAČEK, Radka SVOBODOVÁ VAŘEKOVÁ, Václav HEJRET, Aleš KŘENEK, Ruben ABAGYAN a Jaroslav KOČA. High-quality and universal empirical atomic charges for chemoinformatics applications. Journal of Cheminformatics. London: BIOMED CENTRAL LTD, 2015, roč. 7, DEC, s. 1-10. ISSN 1758-2946. Dostupné z: https://dx.doi.org/10.1186/s13321-015-0107-1.

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.

PRAVDA, Lukáš, Karel BERKA, Radka SVOBODOVÁ VAŘEKOVÁ, David SEHNAL, Michal OTYEPKA a Jaroslav KOČA. MOLE 2.5: Improved Tool for Analysis of Ligand-Accessible Channels. In ISMB/ECCB 2015, Dublin, Ireland. 2015.

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.

PRAVDA, Lukáš, Karel BERKA, Radka SVOBODOVÁ VAŘEKOVÁ, David SEHNAL, Pavel BANÁŠ, Laskowski ROMAN A, Jaroslav KOČA a Michal OTYEPKA. Anatomy of Enzyme Channels. BMC Bioinformatics. England: BioMed Central Ltd, 2014, roč. 15, november, s. "nestránkováno", 8 s. ISSN 1471-2105. Dostupné z: https://dx.doi.org/10.1186/s12859-014-0379-x.

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.

GEIDL, Stanislav, Radka SVOBODOVÁ VAŘEKOVÁ, Lukáš PETRUSEK, David SEHNAL a Jaroslav KOČA. Jaký vliv na přesnost QSPR modelů má metodika přípravy 3D struktury? Případová studie pro predikci pKa. In ENBIK - Národní bioinformatická konference. 2014. ISBN 978-80-7080-883-2.

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.

RAČEK, Tomáš, Radka SVOBODOVÁ VAŘEKOVÁ, Aleš KŘENEK, Tomáš BOUCHAL a Jaroslav KOČA. NEEMP – Tool for parameterization of empirical charge calculation method EEM. In Chemoinformatics Strasbourg Summer School 2014. 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.

RAČEK, Tomáš, Radka SVOBODOVÁ VAŘEKOVÁ a Aleš KŘENEK. Advanced implementation of atomic charge calculation with electronegativity equalization. In SVOČ 2013 v Opavě. 2013.

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.

PRAVDA, Lukáš, Radka SVOBODOVÁ VAŘEKOVÁ, David SEHNAL, Karel BERKA, Michal OTYEPKA a Jaroslav KOČA. MOLE 2.0: Improved Approach for Analysis of Biomacromolecular Channels and Pores. In 21st Annual International Conference on Intelligent Systems for Molecular Biology and 12th European Conference on Computational Biology, Berlin, Germany. 2013.

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.

GEIDL, Stanislav, Roman BERÁNEK, Radka SVOBODOVÁ VAŘEKOVÁ, Tomáš BOUCHAL a Jaroslav KOČA. Predikce pKa pro nově navržené molekuly léků. In ENBIK - Národní bioinformatická konference. 2012. ISBN 978-80-7080-818-4.

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.

RYŠKA, Jan, Sushil Kumar MISHRA, Radka SVOBODOVÁ VAŘEKOVÁ a Jaroslav KOČA. Docking study of matrix metalloproteinase inhibitors. In 9th Discussions in Structural Molecular Biology, Nové Hrady, Czech Republic. 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, Roman BERÁNEK, Radka SVOBODOVÁ VAŘEKOVÁ, Tomáš BOUCHAL, Miroslav BRUMOVSKÝ, Michal KUDERA, Ondřej SKŘEHOTA a Jaroslav KOČA. How the methodology of 3D structure preparation influences the quality of QSPR models? In 7th German Conference on Chemoinformatics. 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.

OPPELT, Jan, Boris TICHÝ, Marek MRÁZ, Radka SVOBODOVÁ VAŘEKOVÁ a Jaroslav KOČA. Zpracování dat z vysoce výkonných sekvenátorů. In Studentská vědecká konference PřF OU. 2011. ISBN 978-80-7368-908-7.

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.

SVOBODOVÁ VAŘEKOVÁ, Radka, David SEHNAL, Lukáš PRAVDA, Jan OPPELT a Jaroslav KOČA. SiteBinder – software tool for superimposing multiple structural motives. In 8th Discussions in Structural Molecular Biology. Nove Hrady, 2010.

NOVOTNÁ JIROUŠKOVÁ, Zuzana, Radka SVOBODOVÁ VAŘEKOVÁ, Jakub VANĚK a Jaroslav KOČA. Electronegativity Equalization Method - Fast Method For Charge Calculation. In Materials Structure, vol. 16, no. 1 (2009). 2009. ISSN 1211-5894.