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Items: 1 to 20 of 36

1.

Molecular Evolution and Diversification of Proteins Involved in miRNA Maturation Pathway.

Moturu TR, Sinha S, Salava H, Thula S, Nodzyński T, Vařeková RS, Friml J, Simon S.

Plants (Basel). 2020 Mar 1;9(3). pii: E299. doi: 10.3390/plants9030299.

2.

PDBe: improved findability of macromolecular structure data in the PDB.

Armstrong DR, Berrisford JM, Conroy MJ, Gutmanas A, Anyango S, Choudhary P, Clark AR, Dana JM, Deshpande M, Dunlop R, Gane P, Gáborová R, Gupta D, Haslam P, Koča 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-Vařeková R, Zaki H, Kleywegt GJ, Velankar S.

Nucleic Acids Res. 2020 Jan 8;48(D1):D335-D343. doi: 10.1093/nar/gkz990.

PMID:
31691821
3.

The bio.tools registry of software tools and data resources for the life sciences.

Ison J, Ienasescu H, Chmura P, Rydza E, Ménager H, Kalaš M, Schwämmle V, Grüning B, Beard N, Lopez R, Duvaud S, Stockinger H, Persson B, Vařeková RS, Raček T, Vondrášek J, Peterson H, Salumets A, Jonassen I, Hooft R, Nyrönen T, Valencia A, Capella S, Gelpí J, Zambelli F, Savakis B, Leskošek B, Rapacki K, Blanchet C, Jimenez R, Oliveira A, Vriend G, Collin O, van Helden J, Løngreen P, Brunak S.

Genome Biol. 2019 Aug 12;20(1):164. doi: 10.1186/s13059-019-1772-6.

4.

Automated Family-Wide Annotation of Secondary Structure Elements.

Midlik A, Hutařová Vařeková I, Hutař J, Moturu TR, Navrátilová V, Koča J, Berka K, Svobodová Vařeková R.

Methods Mol Biol. 2019;1958:47-71. doi: 10.1007/978-1-4939-9161-7_3.

PMID:
30945213
5.

SugarSketcher: Quick and Intuitive Online Glycan Drawing.

Alocci D, Suchánková P, Costa R, Hory N, Mariethoz J, Vařeková RS, Toukach P, Lisacek F.

Molecules. 2018 Dec 5;23(12). pii: E3206. doi: 10.3390/molecules23123206.

6.

MOLEonline: a web-based tool for analyzing channels, tunnels and pores (2018 update).

Pravda L, Sehnal D, Toušek D, Navrátilová V, Bazgier V, Berka K, Svobodová Vareková R, Koca J, Otyepka M.

Nucleic Acids Res. 2018 Jul 2;46(W1):W368-W373. doi: 10.1093/nar/gky309.

7.

Molecular evolution and diversification of the SMXL gene family.

Moturu TR, Thula S, Singh RK, Nodzynski T, Vareková RS, Friml J, Simon S.

J Exp Bot. 2018 Apr 23;69(9):2367-2378. doi: 10.1093/jxb/ery097.

PMID:
29538714
8.

Worldwide Protein Data Bank validation information: usage and trends.

Smart OS, Horský V, Gore S, Svobodová Vařeková R, Bendová V, Kleywegt GJ, Velankar S.

Acta Crystallogr D Struct Biol. 2018 Mar 1;74(Pt 3):237-244. doi: 10.1107/S2059798318003303. Epub 2018 Mar 2.

9.

Validation of ligands in macromolecular structures determined by X-ray crystallography.

Smart OS, Horský V, Gore S, Svobodová Vařeková R, Bendová V, Kleywegt GJ, Velankar S.

Acta Crystallogr D Struct Biol. 2018 Mar 1;74(Pt 3):228-236. doi: 10.1107/S2059798318002541. Epub 2018 Mar 2.

10.

LiteMol suite: interactive web-based visualization of large-scale macromolecular structure data.

Sehnal D, Deshpande M, Vařeková RS, Mir S, Berka K, Midlik A, Pravda L, Velankar S, Koča J.

Nat Methods. 2017 Nov 30;14(12):1121-1122. doi: 10.1038/nmeth.4499. No abstract available.

PMID:
29190272
11.

ChannelsDB: database of biomacromolecular tunnels and pores.

Pravda L, Sehnal D, Svobodová Vareková R, Navrátilová V, Toušek D, Berka K, Otyepka M, Koca J.

Nucleic Acids Res. 2018 Jan 4;46(D1):D399-D405. doi: 10.1093/nar/gkx868.

12.

PDBsum: Structural summaries of PDB entries.

Laskowski RA, Jabłońska J, Pravda L, Vařeková RS, Thornton JM.

Protein Sci. 2018 Jan;27(1):129-134. doi: 10.1002/pro.3289. Epub 2017 Oct 27.

13.

Four simple recommendations to encourage best practices in research software.

Jiménez RC, Kuzak M, Alhamdoosh M, Barker M, Batut B, Borg M, Capella-Gutierrez S, Chue Hong N, Cook M, Corpas M, Flannery M, Garcia L, Gelpí JL, Gladman S, Goble C, González Ferreiro M, Gonzalez-Beltran A, Griffin PC, Grüning B, Hagberg J, Holub P, Hooft R, Ison J, Katz DS, Leskošek B, López Gómez F, Oliveira LJ, Mellor D, Mosbergen R, Mulder N, Perez-Riverol Y, Pergl R, Pichler H, Pope B, Sanz F, Schneider MV, Stodden V, Suchecki R, Svobodová Vařeková R, Talvik HA, Todorov I, Treloar A, Tyagi S, van Gompel M, Vaughan D, Via A, Wang X, Watson-Haigh NS, Crouch S.

F1000Res. 2017 Jun 13;6. pii: ELIXIR-876. doi: 10.12688/f1000research.11407.1. eCollection 2017.

14.

NEEMP: software for validation, accurate calculation and fast parameterization of EEM charges.

Raček T, Pazúriková J, Svobodová Vařeková R, Geidl S, Křenek A, Falginella FL, Horský V, Hejret V, Koča J.

J Cheminform. 2016 Oct 17;8:57. eCollection 2016.

15.

The Eighth Central European Conference "Chemistry towards Biology": Snapshot.

Perczel A, Atanasov AG, Sklenář V, Nováček J, Papoušková V, Kadeřávek P, Žídek L, Kozłowski H, Wątły J, Hecel A, Kołkowska P, Koča J, Svobodová-Vařeková R, Pravda L, Sehnal D, Horský V, Geidl S, Enriz RD, Matějka P, Jeništová A, Dendisová M, Kokaislová A, Weissig V, Olsen M, Coffey A, Ajuebor J, Keary R, Sanz-Gaitero M, van Raaij MJ, McAuliffe O, Waltenberger B, Mocan A, Šmejkal K, Heiss EH, Diederich M, Musioł R, Košmrlj J, Polański J, Jampílek J.

Molecules. 2016 Oct 17;21(10). pii: E1381.

16.

Top 10 metrics for life science software good practices.

Artaza H, Chue Hong N, Corpas M, Corpuz A, Hooft R, Jimenez RC, Leskošek B, Olivier BG, Stourac J, Svobodová Vařeková R, Van Parys T, Vaughan D.

F1000Res. 2016 Aug 16;5. pii: ELIXIR-2000. doi: 10.12688/f1000research.9206.1. eCollection 2016.

17.

High-quality and universal empirical atomic charges for chemoinformatics applications.

Geidl S, Bouchal T, Raček T, Svobodová Vařeková R, Hejret V, Křenek A, Abagyan R, Koča J.

J Cheminform. 2015 Dec 2;7:59. doi: 10.1186/s13321-015-0107-1. eCollection 2015.

18.

Tools and data services registry: a community effort to document bioinformatics resources.

Ison J, Rapacki K, Ménager H, Kalaš M, Rydza E, Chmura P, Anthon C, Beard N, Berka K, Bolser D, Booth T, Bretaudeau A, Brezovsky J, Casadio R, Cesareni G, Coppens F, Cornell M, Cuccuru G, Davidsen K, Vedova GD, Dogan T, Doppelt-Azeroual O, Emery L, Gasteiger E, Gatter T, Goldberg T, Grosjean M, Grüning B, Helmer-Citterich M, Ienasescu H, Ioannidis V, Jespersen MC, Jimenez R, Juty N, Juvan P, Koch M, Laibe C, Li JW, Licata L, Mareuil F, Mičetić I, Friborg RM, Moretti S, Morris C, Möller S, Nenadic A, Peterson H, Profiti G, Rice P, Romano P, Roncaglia P, Saidi R, Schafferhans A, Schwämmle V, Smith C, Sperotto MM, Stockinger H, Vařeková RS, Tosatto SC, de la Torre V, Uva P, Via A, Yachdav G, Zambelli F, Vriend G, Rost B, Parkinson H, Løngreen P, Brunak S.

Nucleic Acids Res. 2016 Jan 4;44(D1):D38-47. doi: 10.1093/nar/gkv1116. Epub 2015 Nov 3.

19.

AtomicChargeCalculator: interactive web-based calculation of atomic charges in large biomolecular complexes and drug-like molecules.

Ionescu CM, Sehnal D, Falginella FL, Pant P, Pravda L, Bouchal T, Svobodová Vařeková R, Geidl S, Koča J.

J Cheminform. 2015 Oct 22;7:50. doi: 10.1186/s13321-015-0099-x. eCollection 2015.

20.

PatternQuery: web application for fast detection of biomacromolecular structural patterns in the entire Protein Data Bank.

Sehnal D, Pravda L, Svobodová Vařeková R, Ionescu CM, Koča J.

Nucleic Acids Res. 2015 Jul 1;43(W1):W383-8. doi: 10.1093/nar/gkv561. Epub 2015 May 26.

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