Radka Svobodová, Ph.D.

Publications that are part of the Web of Science database, possibly also other publications chosen by authors.

2021

• Sillitoe, I; Bordin, N; Dawson, N; Waman, VP; Ashford, P; Scholes, HM; Pang, CSM; Woodridge, L; Rauer, C; Sen, N; Abbasian, M; Le Cornu, S; Lam, SD; Berka, K; Varekova, IH; Svobodova, R; Lees, J; Orengo, CA, 2021: CATH: increased structural coverage of functional space. NUCLEIC ACIDS RESEARCH 49(D1), p. D266 - D273, doi: 10.1093/nar/gkaa1079
• Sehnal, D; Bittrich, S; Deshpande, M; Svobodova, R; Berka, K; Bazgier, V; Velankar, S; Burley, SK; Koca, J; Rose, AS, 2021: Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures. NUCLEIC ACIDS RESEARCH 49(W1), p. W431 - W437, doi: 10.1093/nar/gkab314
• Schindler, O; Racek, T; Marsavelski, A; Koca, J; Berka, K; Svobodova, R, 2021: Optimized SQE atomic charges for peptides accessible via a web application. JOURNAL OF CHEMINFORMATICS 13(1), doi: 10.1186/s13321-021-00528-w
• Midlik, A; Navratilova, V; Moturu, TR; Koca, J; Svobodova, R; Berka, K, 2021: Uncovering of cytochrome P450 anatomy by SecStrAnnotator. SCIENTIFIC REPORTS 11(1), doi: 10.1038/s41598-021-91494-8

2020

• Sehnal, D; Bittrich, S; Velankar, S; Koca, J; Svobodova, R; Burley, SK; Rose, AS, 2020: BinaryCIF and CIFTools-Lightweight, efficient and extensible macromolecular data management. PLOS COMPUTATIONAL BIOLOGY 16(10), doi: 10.1371/journal.pcbi.1008247
• Armstrong, DR; Berrisford, JM; Conroy, MJ; Gutmanas, A; Anyango, S; Choudhary, P; Clark, AR; Dana, JM; Deshpande, M; Dunlop, R; Gane, P; Gaborova, R; Gupta, D; Haslam, P; Koca, J; Mak, L; Mir, S; Mukhopadhyay, A; Nadzirin, N; Nair, S; Paysan-Lafosse, T; Pravda, L; Sehnal, D; Salih, O; Smart, O; Tolchard, J; Varadi, M; Svobodova-Varekova, R; Zaki, H; Kleywegt, GJ; Velankar, S, 2020: PDBe: improved findability of macromolecular structure data in the PDB. NUCLEIC ACIDS RESEARCH 48(D1), p. D335 - D343, doi: 10.1093/nar/gkz990
• Racek, T; Schindler, O; Tousek, D; Horsky, V; Berka, K; Koca, J; Svobodova, R, 2020: Atomic Charge Calculator II: web-based tool for the calculation of partial atomic charges. NUCLEIC ACIDS RESEARCH 48(W1), p. W591 - W596, doi: 10.1093/nar/gkaa367
• Sehnal, D; Svobodova, R; Berka, K; Rose, AS; Burley, SK; Velankar, S; Koca, J, 2020: High-performance macromolecular data delivery and visualization for the web. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 76, p. 1167 - 1173, doi: 10.1107/S2059798320014515
• Sehnal, D; Svobodova, R; Berka, K; Pravda, L; Midlik, A; Koca, J, 2020: Visualization and Analysis of Protein Structures with LiteMol Suite. STRUCTURAL BIOINFORMATICS: METHODS AND PROTOCOLS 2112, p. 1 - 13, doi: 10.1007/978-1-0716-0270-6_1

2018

• Pravda, L; Sehnal, D; Varekova, RS; Navratilova, V; Tousek, D; Berka, K; Otyepka, M; Koca, J, 2018: ChannelsDB: database of biomacromolecular tunnels and pores. NUCLEIC ACIDS RESEARCH 46(D1), p. D399 - D405, doi: 10.1093/nar/gkx868
• Moturu, R.; Thula, S.; Singh, R.; Nodzynski, T.; Svobodová Vareková, R.; Friml, J.; Simon, S.;, 2018: Molecular Evolution and Diversification of SMAX-Like Gene Family. J NEURAL ENG , doi: 10.1093/jxb/ery097
• Pravda, L; Sehnal, D; Toušek, D; Navrátilová, V; Bazgier, V; Berka, K; Svobodová Vareková, R; Koca, J; Otyepka, M, 2018: MOLEonline: a web-based tool for analyzing channels, tunnels and pores (2018 update). NUCLEIC ACIDS RESEARCH , doi: 10.1093/nar/gky309
• Pravda, L; Sehnal, D; Berka, K; Navratilova, V; Tousek, D; Bazgier, V; Varekova, RS; Otyepka, M; Koca, J, 2018: Channelsdb and Moleonline - Database and Tool for Analysis of Biomacromolecular Tunnels and Pores. BIOPHYSICAL JOURNAL 114(3), p. 342A - 343A, doi: 10.1016/j.bpj.2017.11.1912
• Sehnal, D; Deshpande, M; Rose, A; Pravda, L; Midlik, A; Varekova, RS; Mir, S; Berka, K; Velankar, S; Koca, J, 2018: Interactive 3D Macromolecular Structure Data Mining with MolQL and Litemol Suite. BIOPHYSICAL JOURNAL 114(3), p. 47A - 47A, doi: 10.1016/j.bpj.2017.11.308
• Moturu, TR; Thula, S; Singh, RK; Nodzynski, T; Varekova, RS; Friml, J; Simon, S, 2018: Molecular evolution and diversification of the SMXL gene family. JOURNAL OF EXPERIMENTAL BOTANY 69(9), p. 2367 - 2378, doi: 10.1093/jxb/ery097
• Varekova, RS; Midlik, A; Varekova, IH; Hutar, J; Navratilova, V; Koca, J; Berka, K, 2018: Secondary Structure Elements - Annotations and Schematic 2D Visualizations Stable for Individual Protein Families. BIOPHYSICAL JOURNAL 114(3), p. 46A - 47A

2017

• Varekova, RS; Horsky, V; Sehnal, D; Bendova, V; Pravda, L; Koca, J, 2017: Quo Vadis, Biomacromolecular Structure Quality. BIOPHYSICAL JOURNAL 112(3), p. 346A - 347A
• Berka, K; Sehnal, D; Bazgier, V; Pravda, L; Svobodova-Varekova, R; Otyepka, M; Koca, J, 2017: Mole 2.5-Tool for Detection and Analysis of Macromolecular Pores and Channels. BIOPHYSICAL JOURNAL 112(3), p. 292A - 293A
• Pravda, L; Sehnal, D; Varekova, RS; Koca, J, 2017: Effective on-Demand Mining of Structural Databases. BIOPHYSICAL JOURNAL 112(3), p. 348A - 348A
• Sehnal, D; Deshpande, M; Varekova, RS; Mir, S; Berka, K; Midlik, A; Pravda, L; Velankar, S; Koca, J, 2017: Real-Time Interactive Visualisation of Large Macromolecular Assemblies and Molecular Machines at Atomic Resolution. BIOPHYSICAL JOURNAL 112(3), p. 178A - 178A

2016

• Perczel, A; Atanasov, AG; Sklenar, V; Novacek, J; Papouskova, V; Kaderavek, P; Zidek, L; Kozlowski, H; Watly, J; Hecel, A; Kolkowska, P; Koca, J; Svobodova-Varekova, R; Pravda, L; Sehnal, D; Horsky, V; Geidl, S; Enriz, RD; Matejka, P; Jenistova, A; Dendisova, M; Kokaislova, A; Weissig, V; Olsen, M; Coffey, A; Ajuebor, J; Keary, R; Sanz-Gaitero, M; Raaij, MJ; McAuliffe, O; Waltenberger, B; Mocan, A; Smejkal, K; Heis, EH; Diederich, M; Musiol, R; Kosmrlj, J; Polanski, J; Jampilek, J, 2016: The Eighth Central European Conference ´´Chemistry towards Biology´´: Snapshot. MOLECULES 21(10), doi: 10.3390/molecules21101381
• Adams, P; Aertgeerts, K; Bauer, C; Bell, JA; Berman, HM; Bhat, TN; Blaney, JM; Bolton, E; Bricogne, G; Brown, D; Burley, SK; Case, DA; Clark, KL; Darden, T; Emsley, P; Feher, VA; Feng, ZK; Groom, CR; Harris, SF; Hendle, J; Holder, T; Joachimiak, A; Kleywegt, GJ; Krojer, T; Marcotrigiano, J; Mark, AE; Markley, JL; Miller, M; Minor, W; Montelion, GT; Murshudov, G; Nakagawa, A; Nakamura, H; Nicholls, A; Nicklaus, M; Nolte, RT; Padyana, AK; Peishoff, CE; Pieniazek, S; Read, RJ; Shao, CH; Sheriff, S; Smart, O; Soisson, S; Spurlino, J; Stouch, T; Svobodova, R; Tempel, W; Terwilliger, TC; Tronrud, D; Velankar, S; Ward, SC; Warren, GL; Westbrook, JD; Williams, P; Yang, HW; Young, J, 2016: Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop. STRUCTURE 24(4), doi: 10.1016/j.str.2016.02.017
• Ison, J; Rapacki, K; Menager, H; Kalas, M; Rydza, E; Chmura, P; Anthon, C; Beard, N; Berka, K; Bolser, D; Booth, T Bretaudeau, A; Brezovsky, J; Casadio, R; Cesareni, G; Copens, F; Cornell, M Cuccuru, G; Davidsen, K; Della Vedova, G; Dogan, T; Doppelt-Azeroual, O; Emery, L; Gasteiger, E; Gatter, T; Goldberg, T; Grosjean, M; Gruning, B; Helmer-Citterich, M; Ienasescu, H; Ioannidis, V; Jespersen, MC; Jimenz, R; Juty, N; Juvan, P; Koch, M; Laibe, C; Li, JW; Licata, L; Mareuil, F; Micetic, I; Friborg, RM; Moretti, S; Morris, C; Moller, S; Nenadic, A; Peterson, H; Profiti, G; Rice, P; Romano, P; Roncaglia, P; Saidi, R; Schafferhans, A; Schwammle, V; Smith, C; Sperotto, MM; Stockinger, H; Varekova, RS; Tosatto, SCE; de la Torre, V; Uva, P; Via, A; Yachdav, G; Zambelli, F; Vriend, G; Rost, B; Parkinson, H; Longreen, P; Brunak, S , 2016: Tools and data services registry: a community effort to document bioinformatics resources. NUCLEIC ACIDS RESEARCH 44(D1), doi: 10.1093/nar/gkv1116
• Racek, T; Pazurikova, J; Varekova, RS; Geidl, S; Krenek, A; Falginella, FL; Horsky, V; Hejret, V; Koca, J, 2016: NEEMP: software for validation, accurate calculation and fast parameterization of EEM charges. JOURNAL OF CHEMINFORMATICS 8, doi: 10.1186/s13321-016-0171-1

2015

• Ionescu, CM; Sehnal, D; Falginella, FL; Pant, P; Pravda, L; Bouchal, T; Varekova, RS; Geidl, S; Koca, J, 2015: AtomicChargeCalculator: interactive web-based calculation of atomic charges in large biomolecular complexes and drug-like molecules. JOURNAL OF CHEMINFORMATICS 7, doi: 10.1186/s13321-015-0099-x
• GEIDL, S; BOUCHAL, T; RAČEK, T; SVOBODOVA VAREKOVA, R; HEJRET, V; KŘENEK, A; ABAGYAN, R; KOČA, J, 2015: High-quality and universal empirical atomic charges for chemoinformatics applications. JOURNAL OF CHEMINFORMATICS 7, doi: 10.1186/s13321-015-0107-1

2012

• Ionescu, CM; Varekova, RS; Prehn, JHM; Huber, HJ; Koca, J, 2012: Charge Profile Analysis Reveals That Activation of Pro-apoptotic Regulators Bax and Bak Relies on Charge Transfer Mediated Allosteric Regulation. PLOS COMPUTATIONAL BIOLOGY 8(6), doi: 10.1371/journal.pcbi.1002565
• Sehnal, D; Varekova, RS; Huber, HJ; Geidl, S; Ionescu, CM; Wimmerova, M; Koca, J, 2012: SiteBinder: An Improved Approach for Comparing Multiple Protein Structural Motifs. JOURNAL OF CHEMICAL INFORMATION AND MODELING 52(2), p. 343 - 359, doi: 10.1021/ci200444d

2011

• Varekova, RS; Geidl, S; Ionescu, CM; Skrehota, O; Kudera, M; Sehnal, D; Bouchal, T; Abagyan, R; Huber, HJ; Koca, J, 2011: 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 51(8), p. 1795 - 1806, doi: 10.1021/ci200133w

• Connect and align ELIXIR Nodes to deliver sustainable FAIR life-science data management services, , 2020 - 2023
• Czech National Infrastructure for Biological Data, , 2020 - 2022
• ELIXIR-CZ: Budování kapacit (CZ.02.1.01/0.0/0.0/16_013/0001777), Ministerstvo školství, mládeže a tělovýchovy ČR, 2017 - 2021
• Czech National Infrastructure for Biological Data (LM2015047), Ministerstvo školství, mládeže a tělovýchovy ČR, 2016 - 2019
• SYLICA - Synergies of Life and Material Sciences to Create a New Future (286154), Evropská unie, 2011 - 2015
• InterBioNet - Podpora mezinárodní a mezisektorové spolupráce ve výzkumu a vývoji v oblasti věd o živé přírodě (CZ.1.07/2.4.00/17.0042), Ministerstvo školství, mládeže a tělovýchovy ČR, 2011 - 2014
• Molekulární a strukturní biologie vybraných cytostatik. Od mechanických studií k chemoterapii rakoviny (GD301/09/H004), Grantová agentura ČR, 2009 - 2012
• REAKTIVACE - Výzkum reaktivace acetylcholinesterasy metodami výpočetní chemie (OVMASUN200901), Ministerstvo obrany ČR, 2009 - 2012