Výpis publikací

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://dx.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://dx.doi.org/10.1093/nar/gky949.

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://dx.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://dx.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://dx.doi.org/10.1093/nar/gky309.

LASKOWSKI, R.A.; Jagoda JABŁOŃSKA; Lukáš PRAVDA; Radka SVOBODOVÁ VAŘEKOVÁ a Janet M THORNTON. PDBsum: Structural summaries of PDB entries. Protein Science. HOBOKEN: WILEY, 2018, roč. 27, č. 1, s. 129-134. ISSN 0961-8368. Dostupné z: https://dx.doi.org/10.1002/pro.3289.

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.

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.

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.

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.

ŠÍMA, Michal; Marian NOVOTNÝ; Lukáš PRAVDA; Petra SUMOVÁ; Iva ROHOUŠOVÁ a Petr VOLF. The Diversity of Yellow-Related Proteins in Sand Flies (Diptera: Psychodidae). PLOS ONE. San Francisco: Public Library of Science, 2016, roč. 11, č. 11, s. nestránkováno, 17 s. ISSN 1932-6203. Dostupné z: https://dx.doi.org/10.1371/journal.pone.0166191.

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.

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.

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.

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.

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; 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.

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.