David Sehnal, Ph.D.

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

2021

• 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

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
• 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

2019

• Sehnal, D; Grant, OC, 2019: Rapidly Display Glycan Symbols in 3D Structures: 3D-SNFG in LiteMol. JOURNAL OF PROTEOME RESEARCH 18(2), p. 770 - 774, doi: 10.1021/acs.jproteome.8b00473
• Burley, SK; Berman, HM; Bhikadiya, C; Bi, CX; Chen, L; Di Costanzo, L; Christie, C; Duarte, JM; Dutta, S; Feng, ZK; Ghosh, S; Goodsell, DS; Green, RK; Guranovic, V; Guzenko, D; Hudson, BP; Liang, YH; Lowe, R; Peisach, E; Periskova, I; Randle, C; Rose, A; Sekharan, M; Shao, CH; Tao, YP; Valasatava, Y; Voigt, M; Westbrook, J; Young, J; Zardecki, C; Zhuravleva, M; Kurisu, G; Nakamura, H; Kengaku, Y; Cho, H; Sato, J; Kim, JY; Ikegawa, Y; Nakagawa, A; Yamashita, R; Kudou, T; Bekker, GJ; Suzuki, H; Iwata, T; Yokochi, M; Kobayashi, N; Fujiwara, T; Velankar, S; Kleywegt, GJ; Anyango, S; Armstrong, DR; Berrisford, JM; Conroy, MJ; Dana, JM; Deshpande, M; Gane, P; Gaborova, R; Gupta, D; Gutmanas, A; Koca, J; Mak, L; Mir, S; Mukhopadhyay, A; Nadzirin, N; Nair, S; Patwardhan, A; Paysan-Lafosse, T; Pravda, L; Salih, O; Sehnal, D; Varadi, M; Varekova, R; Markley, JL; Hoch, JC; Romero, PR; Baskaran, K; Maziuk, D; Ulrich, EL; Wedell, JR; Yao, HY; Livny, M; Ioannidis, YE, 2019: Protein Data Bank: the single global archive for 3D macromolecular structure data. NUCLEIC ACIDS RESEARCH 47(D1), p. D520 - D528, doi: 10.1093/nar/gky949

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
• Mir, S; Alhroub, Y; Anyango, S; Armstrong, DR; Berrisford, JM; Clark, AR; Conroy, MJ; Dana, JM; Deshpande, M; Gupta, D; Gutmanas, A; Haslam, P; Mak, L; Mukhopadhyay, A; Nadzirin, N; Paysan-Lafosse, T; Sehnal, D; Sen, S; Smart, OS; Varadi, M; Kleywegt, GJ; Velankar, S, 2018: PDBe: towards reusable data delivery infrastructure at protein data bank in Europe. NUCLEIC ACIDS RESEARCH 46(D1), p. D486 - D492, doi: 10.1093/nar/gkx1070
• 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
• Rose, AS; Sehnal, D; Bliven, S; Burley, SK; Velankar, S, 2018: Molql: Towards a Common General Purpose Molecular Query Language. BIOPHYSICAL JOURNAL 114(3), p. 342A - 342A

2017

• Pravda, L; Sehnal, D; Varekova, RS; Koca, J, 2017: Effective on-Demand Mining of Structural Databases. BIOPHYSICAL JOURNAL 112(3), p. 348A - 348A
• 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
• 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
• Sehnal, D; Deshpande, M; Varekova, RS; Mir, S; Berka, K; Midlik, A; Pravda, L; Velankar, S; Koca, J, 2017: LiteMol suite: interactive web-based visualization of large-scale macromolecular structure data. NATURE METHODS 14(12), p. 1121 - 1122, doi: 10.1038/nmeth.4499
• 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

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
• Sehnal, D; Varekova, RS; Pravda, L; Ionescu, CM; Geidl, S; Horsky, V; Jaiswal, D; Wimmerova, M; Koca, J, 2015: ValidatorDB: database of up-to-date validation results for ligands and non-standard residues from the Protein Data Bank. NUCLEIC ACIDS RESEARCH 43(D1), p. D369 - D375, doi: 10.1093/nar/gku1118

• 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