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Items: 19

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.

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.

4.

Rapidly Display Glycan Symbols in 3D Structures: 3D-SNFG in LiteMol.

Sehnal D, Grant OC.

J Proteome Res. 2019 Feb 1;18(2):770-774. doi: 10.1021/acs.jproteome.8b00473. Epub 2018 Sep 19.

PMID:
30179493
5.

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.

6.

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
7.

PDBe: towards reusable data delivery infrastructure at protein data bank in Europe.

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.

Nucleic Acids Res. 2018 Jan 4;46(D1):D486-D492. doi: 10.1093/nar/gkx1070.

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.

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.

10.

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.

11.

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.

12.

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.

13.

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.

14.

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.

15.

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.

16.

Predicting p Ka values from EEM atomic charges.

Vařeková RS, Geidl S, Ionescu CM, Skřehota O, Bouchal T, Sehnal D, Abagyan R, Koča J.

J Cheminform. 2013 Apr 10;5(1):18. doi: 10.1186/1758-2946-5-18.

17.

MOLEonline 2.0: interactive web-based analysis of biomacromolecular channels.

Berka K, Hanák O, Sehnal D, Banás P, Navrátilová V, Jaiswal D, Ionescu CM, Svobodová Vareková R, Koca J, Otyepka M.

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W222-7. doi: 10.1093/nar/gks363. Epub 2012 May 2.

18.

SiteBinder: an improved approach for comparing multiple protein structural motifs.

Sehnal D, Vařeková RS, Huber HJ, Geidl S, Ionescu CM, Wimmerová M, Koča J.

J Chem Inf Model. 2012 Feb 27;52(2):343-59. doi: 10.1021/ci200444d. Epub 2012 Feb 8.

PMID:
22296449
19.

Predicting pK(a) values of substituted phenols from atomic charges: comparison of different quantum mechanical methods and charge distribution schemes.

Svobodová Vareková R, Geidl S, Ionescu CM, Skrehota O, Kudera M, Sehnal D, Bouchal T, Abagyan R, Huber HJ, Koca J.

J Chem Inf Model. 2011 Aug 22;51(8):1795-806. doi: 10.1021/ci200133w. Epub 2011 Aug 1.

PMID:
21761919

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