Výpis publikací

SLANINÁKOVÁ, Terézia; Zachary CHARLOP-POWERS; Viktoriia DOSHCHENKO; Alexander S. ROSE; Adam MIDLIK; Anna SEKULA; Neli FONSECA; Kyle L. MORRIS; Stephen K. BURLEY; Sameer VELANKAR; Jennifer FLEMING; Brinda VALLAT; Ludovic AUTIN a David SEHNAL. MolViewStories: Interactive molecular storytelling. PROTEIN SCIENCE. HOBOKEN: WILEY, 2026, roč. 35, č. 4, s. 1-13. ISSN 0961-8368. Dostupné z: https://doi.org/10.1002/pro.70540.

MIDLIK, Adam; Sebastian BITTRICH; Jennifer R FLEMING; Sreenath NAIR; Sameer VELANKAR; Stephen K BURLEY; Jasmine Y YOUNG; Brinda VALLAT a David SEHNAL. MolViewSpec: a Mol* extension for describing and sharing molecular visualizations. Nucleic Acids Research. Oxford: Oxford University Press, 2025, roč. 53, W1, s. "W408"-"W414", 7 s. ISSN 0305-1048. Dostupné z: https://doi.org/10.1093/nar/gkaf370.

SLANINÁKOVÁ, Terézia; Eva MARŠÁLKOVÁ; Katarína GREŠOVÁ; Aleš KŘENEK; Jaroslav OĽHA; Tomáš PAVLÍK; Pavlína ŠPRINGEROVÁ; David SEHNAL a Matej ANTOL. Refining Structure-Based Search in AlphaFold DB: Including confidence metrics into AlphaFind. In CZECH PHD BIOINFORMATICS CONFERENCE. 2025. Dostupné z: https://doi.org/10.5281/zenodo.15103129.

BITTRICH, Sebastian; Alexander S ROSE; David SEHNAL; Jose M DUARTE; Yana ROSE; Joan SEGURA; Dennis W PIEHL; Brinda VALLAT; Chenghua SHAO; Charmi BHIKADIYA; Jesse LIANG; Mark MA; David S GOODSELL; Stephen K BURLEY a Shuchismita DUTTA. Visualizing and analyzing 3D biomolecular structures using Mol* at RCSB.org: Influenza A H5N1 virus proteome case study. Protein Science. Wiley, 2025, roč. 34, č. 4, s. "e70093", 21 s. ISSN 0961-8368. Dostupné z: https://doi.org/10.1002/pro.70093.

ŠPAČKOVÁ, Anna; Václav BAZGIER; Tomáš RAČEK; David SEHNAL; Radka SVOBODOVÁ a Karel BERKA. Analysis and Visualization of Protein Channels, Tunnels, and Pores with MOLEonline and ChannelsDB 2.0. In Lisacek, Frédérique. Protein Bioinformatics. 1. vyd. New York: Humana Press, 2024, s. 219-233. Methods in Molecular Biology 2836. ISBN 978-1-0716-4006-7. Dostupné z: https://doi.org/10.1007/978-1-0716-4007-4_12.

BITTRICH, Sebastian; Adam MIDLIK; Mihaly VARADI; Sameer VELANKAR; Stephen K BURLEY; Jasmine Y YOUNG; David SEHNAL a Brinda VALLAT. Describing and Sharing Molecular Visualizations Using the MolViewSpec Toolkit. Current Protocols. Wiley, 2024, roč. 4, č. 7, s. 1-23. ISSN 2691-1299. Dostupné z: https://doi.org/10.1002/cpz1.1099.

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://doi.org/10.1093/nar/gkad1012.

ROSE, Alexander; David SEHNAL; David S GOODSELL a Ludovic AUTIN. Mesoscale explorer: Visual exploration of large-scale molecular models. Protein Science. Wiley, 2024, roč. 33, č. 10, s. 1-15. ISSN 0961-8368. Dostupné z: https://doi.org/10.1002/pro.5177.

CHARESHNEU, Aliaksei; Alessio CANTARA; Dominik TICHY a David SEHNAL. Visualizing Volumetric and Segmentation Data using Mol* Volumes & Segmentations 2.0. Current Protocols. Wiley, 2024, roč. 4, č. 12, s. 1-34. ISSN 2691-1299. Dostupné z: https://doi.org/10.1002/cpz1.70070.

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.

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://doi.org/10.1093/nar/gkad411.

MIDLIK, Adam; Sreenath NAIR; Stephen ANYANGO; Mandar DESHPANDE; David SEHNAL; Mihaly VARADI a Sameer VELANKAR. PDBImages: a command-line tool for automated macromolecular structure visualization. Bioinformatics. Oxford: Oxford University Press, 2023, roč. 39, č. 12, s. 1-4. ISSN 1367-4803. Dostupné z: https://doi.org/10.1093/bioinformatics/btad744.

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

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://doi.org/10.1002/pro.4439.

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://doi.org/10.1093/nar/gkab314.

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://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 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; 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 Book of abstracts - 1st Student Conference in Structural Biology. 2021.

SEHNAL, David; Sebastian BITTRICH; Sameer VELANKAR; Jaroslav KOČA; Radka SVOBODOVÁ; Stephen K. BURLEY a Alexander S. ROSE. BinaryCIF and CIFTools-Lightweight, efficient and extensible macromolecular data management. PLoS Computational Biology. San Francisco: Public Library of Science, 2020, roč. 16, č. 10, s. 1-13. ISSN 1553-734X. Dostupné z: https://doi.org/10.1371/journal.pcbi.1008247.

SEHNAL, David; Radka SVOBODOVÁ; Karel BERKA; Alexander S. ROSE; Stephen K. BURLEY; Sameer VELANKAR a Jaroslav KOČA. High-performance macromolecular data delivery and visualization for the web. Acta Crystallographica Section D: Structural Biology. Chester: International Union of Crystallography, 2020, roč. 76, December 2020, s. 1167-1173. ISSN 2059-7983. Dostupné z: https://doi.org/10.1107/S2059798320014515.

ARMSTRONG, David R.; John M. BERRISFORD; Matthew J. CONROY; Aleksandras GUTMANAS; Stephen ANYANGO; Preeti CHOUDHARY; Alice R. CLARK; Jose M. DANA; Mandar DESHPANDE; Roisin DUNLOP; Paul GANE; Romana GÁBOROVÁ; Deepti GUPTA; Pauline HASLAM; Jaroslav KOČA; Lora MAK; Saqib MIR; Abhik MUKHOPADHYAY; Nurul NADZIRIN; Sreenath NAIR; Typhaine PAYSAN-LAFOSSE; Lukas PRAVDA; David SEHNAL; Osman SALIH; Oliver SMART; James TOLCHARD; Mihaly VARADI; Radka SVOBODOVÁ; Hossam ZAKI; Gerard J. KLEYWEGT a Sameer VELANKAR. PDBe: improved findability of macromolecular structure data in the PDB. Nucleic acids research. Oxford: Oxford University Press, 2020, roč. 48, D1, s. "D335"-"D343", 9 s. ISSN 0305-1048. Dostupné z: https://doi.org/10.1093/nar/gkz990.

SEHNAL, David; Radka SVOBODOVÁ; K. BERKA; Lukáš PRAVDA; Adam MIDLIK a Jaroslav KOČA. Visualization and Analysis of Protein Structures with LiteMol Suite. Online. In STRUCTURAL BIOINFORMATICS: METHODS AND PROTOCOLS. TOTOWA: HUMANA PRESS INC, 2020, s. 1-13. 2112. ISBN 978-1-0716-0270-6. Dostupné z: https://doi.org/10.1007/978-1-0716-0270-6_1.

BURLEY, S.K.; H.M. BERMAN; C. BHIKADIYA; C.X. BI; L. CHEN; L. DI COSTANZO; C. CHRISTIE; J.M. DUARTE; S. DUTTA; Z.K. FENG; S. GHOSH; D.S. GOODSELL; R.K. GREEN; V. GURANOVIC; D. GUZENKO; B.P. HUDSON; Y.H. LIANG; R. LOWE; E. PEISACH; I. PERISKOVA; C. RANDLE; A. ROSE; M. SEKHARAN; CH. SHAO; Y.P. TAO; Y. VALASATAVA; M. VOIGT; J. WESTBROOK; J. YOUNG; C. ZARDECKI; M. ZHURAVLEVA; G. KURISU; H. NAKAMURA; Y. KENGAKU; H. CHO; J. SATO; J.Y. KIM; Y. IKEGAWA; A. NAKAGAWA; R. YAMASHITA; T. KUDOU; G.J. BEKKER; H. SUZUKI; T. IWATA; M. YOKOCHI; N. KOBAYASHI; T. FUJIWARA; S. VELANKAR; G.J. KLEYWEGT; S. ANYANGO; D.R. ARMSTRONG; J.M. BERRISFORD; M.J. CONROY; J.M. DANA; M. DESHPANDE; P. GANE; Romana GÁBOROVÁ; D. GUPTA; A. GUTMANAS; Jaroslav KOČA; L. MAK; S. MIR; A. MUKHOPADHYAY; N. NADZIRIN; S. NAIR; A. PATWARDHAN; T. PAYSAN-LAFOSSE; Lukáš PRAVDA; O. SALIH; David SEHNAL; M. VARADI; Radka SVOBODOVÁ VAŘEKOVÁ; J.L. MARKLEY; J.C. HOCH; P.R. ROMERO; K. BASKARAN; D. MAZIUK; E.L. ULRICH; J.R. WEDELL; H.Y. YAO; M. LIVNY a Y.E. IOANNIDIS. Protein Data Bank: the single global archive for 3D macromolecular structure data. Nucleic Acids Research. Oxford: Oxford University Press, 2019, roč. 47, D1, s. "D520"-"D528", 9 s. ISSN 0305-1048. Dostupné z: https://doi.org/10.1093/nar/gky949.

SEHNAL, David a O.C. GRANT. Rapidly Display Glycan Symbols in 3D Structures: 3D-SNFG in LiteMol. Journal of Proteome Research. Washington, USA: AMER CHEMICAL SOC, 2019, roč. 18, č. 2, s. 770-774. ISSN 1535-3893. Dostupné z: https://doi.org/10.1021/acs.jproteome.8b00473.

PRAVDA, Lukáš; David SEHNAL; Radka SVOBODOVÁ VAŘEKOVÁ; Veronika NAVRÁTILOVÁ; Dominik TOUŠEK; Karel BERKA; Michal OTYEPKA a Jaroslav KOČA. ChannelsDB: database of biomacromolecular tunnels and pores. Nucleic Acids Research. Oxford: Oxford University Press, 2018, roč. 46, D1, s. "D399"-"D405", 7 s. ISSN 0305-1048. Dostupné z: https://doi.org/10.1093/nar/gkx868.

SEHNAL, David; M DESHPANDE; A ROSE; Lukáš PRAVDA; Adam MIDLIK; Radka SVOBODOVÁ VAŘEKOVÁ; S MIR; K BERKA; S VELANKAR a Jaroslav KOČA. Interactive 3D Macromolecular Structure Data Mining with MolQL and Litemol Suite. In 62nd Annual Meeting of the Biophysical-Society. 2018. Dostupné z: https://doi.org/10.1016/j.bpj.2017.11.308.

PRAVDA, Lukáš; David SEHNAL; Dominik TOUŠEK; Veronika NAVRÁTILOVÁ; Václav BAZGIER; Karel BERKA; Radka SVOBODOVÁ VAŘEKOVÁ; Jaroslav KOČA a Michal OTYEPKA. MOLEonline: a web-based tool for analyzing channels, tunnels and pores (2018 update). Nucleic Acids Research. Oxford: Oxford University Press, 2018, roč. 46, W1, s. "W368"-"W373", 6 s. ISSN 0305-1048. Dostupné z: https://doi.org/10.1093/nar/gky309.

ROSE, A.S.; David SEHNAL; S. BLIVEN; S.K. BURLEY a S. VELANKAR. Molql: Towards a Common General Purpose Molecular Query Language. In 62nd Annual Meeting of the Biophysical-Society. 2018. ISSN 0006-3495. Dostupné z: https://doi.org/10.1016/j.bpj.2017.11.1910.

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.

MIR, S.; Y. ALHROUB; S. ANYANGO; D.R. ARMSTRONG; J.M. BERRISFORD; A.R. CLARK; M.J. CONROY; J.M. DANA; M. DESHPANDE; D. GUPTA; A. GUTMANAS; P. HASLAM; L. MAK; A. MUKHOPADHYAY; N. NADZIRIN; T. PAYSAN-LAFOSSE; David SEHNAL; S. SEN; O.S. SMART; M. VARADI; G.J. KLEYWEGT a S. VELANKAR. PDBe: towards reusable data delivery infrastructure at protein data bank in Europe. Nucleic Acids Research. Oxford: Oxford University Press, 2018, roč. 46, D1, s. "D486"-"D492", 7 s. ISSN 0305-1048. Dostupné z: https://doi.org/10.1093/nar/gkx1070.

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://doi.org/10.1038/nmeth.4499.

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://doi.org/10.1016/j.bpj.2016.11.1880.

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.

TENGLER, Szymon a David SEHNAL. Method of Solving the Volume Between Triangulated Mesh Surfaces. In Swiatek, J; Borzemski, L; Grzech, A; Wilimowska, Z. INFORMATION SYSTEMS ARCHITECTURE AND TECHNOLOGY, ISAT 2015, PT III. BERLIN: SPRINGER-VERLAG BERLIN, 2016, s. 53-62. ISBN 978-3-319-28562-7. Dostupné z: https://doi.org/10.1007/978-3-319-28564-1_5.

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://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://doi.org/10.3390/molecules21101381.

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://doi.org/10.1186/s13321-015-0099-x.

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://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://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://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://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.

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://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://doi.org/10.1186/1758-2946-5-18.

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.

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://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.

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://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; 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.

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.