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Best matches for Jaroslav Koča:

ChannelsDB: database of biomacromolecular tunnels and pores. Pravda L et al. Nucleic Acids Res. (2018)

Three-dimensional homology model of GlcNAc-TV glycosyltransferase. Janoš P et al. Glycobiology. (2016)

MOLEonline: a web-based tool for analyzing channels, tunnels and pores (2018 update). Pravda L et al. Nucleic Acids Res. (2018)

Search results

Items: 1 to 20 of 104

1.

The CH-π interaction in protein - carbohydrate binding: Bioinformatics and in vitro quantification.

Houser J, Kozmon S, Mishra D, Hammerová Z, Wimmerová M, Koca J.

Chemistry. 2020 Mar 24. doi: 10.1002/chem.202000593. [Epub ahead of print]

PMID:
32208534
2.

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
3.

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
4.

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.

5.

ValTrendsDB: bringing Protein Data Bank validation information closer to the user.

Horský V, Bendová V, Toušek D, Koča J, Svobodová R.

Bioinformatics. 2019 Dec 15;35(24):5389-5390. doi: 10.1093/bioinformatics/btz532.

6.

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
7.

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.

8.
9.

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.

10.

How Mycobacterium tuberculosis Galactofuranosyl Transferase 2 (GlfT2) Generates Alternating β-(1-6) and β-(1-5) Linkages: A QM/MM Molecular Dynamics Study of the Chemical Steps.

Janoš P, Kozmon S, Tvaroška I, Koča J.

Chemistry. 2018 May 11;24(27):7051-7059. doi: 10.1002/chem.201800558. Epub 2018 Apr 30.

PMID:
29575294
11.

Behavior of BsoBI endonuclease in the presence and absence of DNA.

Štěpán J, Kabelka I, Koča J, Kulhánek P.

J Mol Model. 2017 Dec 20;24(1):22. doi: 10.1007/s00894-017-3557-8.

PMID:
29264670
12.

Influence of Trp flipping on carbohydrate binding in lectins. An example on Aleuria aurantia lectin AAL.

Houser J, Kozmon S, Mishra D, Mishra SK, Romano PR, Wimmerová M, Koča J.

PLoS One. 2017 Dec 12;12(12):e0189375. doi: 10.1371/journal.pone.0189375. eCollection 2017.

13.

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
14.

Automated Training of ReaxFF Reactive Force Fields for Energetics of Enzymatic Reactions.

Trnka T, Tvaroška I, Koča J.

J Chem Theory Comput. 2018 Jan 9;14(1):291-302. doi: 10.1021/acs.jctc.7b00870. Epub 2017 Dec 6.

PMID:
29156140
15.

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.

16.

CrocoBLAST: Running BLAST efficiently in the age of next-generation sequencing.

Tristão Ramos RJ, de Azevedo Martins AC, da Silva Delgado G, Ionescu CM, Ürményi TP, Silva R, Koca J.

Bioinformatics. 2017 Nov 15;33(22):3648-3651. doi: 10.1093/bioinformatics/btx465.

PMID:
29036546
17.

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.

18.

Different QM/MM Approaches To Elucidate Enzymatic Reactions: Case Study on ppGalNAcT2.

Janoš P, Trnka T, Kozmon S, Tvaroška I, Koča J.

J Chem Theory Comput. 2016 Dec 13;12(12):6062-6076. Epub 2016 Nov 4.

PMID:
27787999
19.

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.

20.

Three-dimensional homology model of GlcNAc-TV glycosyltransferase.

Janoš P, Kozmon S, Tvaroška I, Koca J.

Glycobiology. 2016 Jul;26(7):757-771. doi: 10.1093/glycob/cww010. Epub 2016 Jan 27.

PMID:
26821880

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