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Items: 17

1.

Visualization and Analysis of Protein Structures with LiteMol Suite.

Sehnal D, Svobodová R, Berka K, Pravda L, Midlik A, Koča J.

Methods Mol Biol. 2020;2112:1-13. doi: 10.1007/978-1-0716-0270-6_1.

PMID:
32006274
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.

PDBe-KB: a community-driven resource for structural and functional annotations.

PDBe-KB consortium .

Nucleic Acids Res. 2020 Jan 8;48(D1):D344-D353. doi: 10.1093/nar/gkz853.

4.

Finding enzyme cofactors in Protein Data Bank.

Mukhopadhyay A, Borkakoti N, Pravda L, Tyzack JD, Thornton JM, Velankar S.

Bioinformatics. 2019 Sep 15;35(18):3510-3511. doi: 10.1093/bioinformatics/btz115.

5.

Protein Data Bank: the single global archive for 3D macromolecular structure data.

wwPDB consortium .

Nucleic Acids Res. 2019 Jan 8;47(D1):D520-D528. doi: 10.1093/nar/gky949.

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.

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
8.

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.

9.

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.

10.

The Diversity of Yellow-Related Proteins in Sand Flies (Diptera: Psychodidae).

Sima M, Novotny M, Pravda L, Sumova P, Rohousova I, Volf P.

PLoS One. 2016 Nov 3;11(11):e0166191. doi: 10.1371/journal.pone.0166191. eCollection 2016.

11.

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.

12.

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.

13.

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.

14.

Anatomy of enzyme channels.

Pravda L, Berka K, Svobodová Vařeková R, Sehnal D, Banáš P, Laskowski RA, Koča J, Otyepka M.

BMC Bioinformatics. 2014 Nov 18;15:379. doi: 10.1186/s12859-014-0379-x.

15.

ValidatorDB: database of up-to-date validation results for ligands and non-standard residues from the Protein Data Bank.

Sehnal D, Svobodová Vařeková R, Pravda L, Ionescu CM, Geidl S, Horský V, Jaiswal D, Wimmerová M, Koča J.

Nucleic Acids Res. 2015 Jan;43(Database issue):D369-75. doi: 10.1093/nar/gku1118. Epub 2014 Nov 11.

16.

MotiveValidator: interactive web-based validation of ligand and residue structure in biomolecular complexes.

Vařeková RS, Jaiswal D, Sehnal D, Ionescu CM, Geidl S, Pravda L, Horský V, Wimmerová M, Koča J.

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W227-33. doi: 10.1093/nar/gku426. Epub 2014 May 21.

17.

MOLE 2.0: advanced approach for analysis of biomacromolecular channels.

Sehnal D, Svobodová Vařeková R, Berka K, Pravda L, Navrátilová V, Banáš P, Ionescu CM, Otyepka M, Koča J.

J Cheminform. 2013 Aug 16;5(1):39. doi: 10.1186/1758-2946-5-39.

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