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Items: 1 to 20 of 95

1.

Outer membrane phospholipase A's roles in Helicobacter pylori acid adaptation.

Vollan HS, Tannæs T, Caugant DA, Vriend G, Bukholm G.

Gut Pathog. 2017 Jun 12;9:36. doi: 10.1186/s13099-017-0184-y. eCollection 2017.

2.

CorNet: Assigning function to networks of co-evolving residues by automated literature mining.

van den Bergh T, Tamo G, Nobili A, Tao Y, Tan T, Bornscheuer UT, Kuipers RKP, Vroling B, de Jong RM, Subramanian K, Schaap PJ, Desmet T, Nidetzky B, Vriend G, Joosten HJ.

PLoS One. 2017 May 18;12(5):e0176427. doi: 10.1371/journal.pone.0176427. eCollection 2017.

3.

NewProt - a protein engineering portal.

Schwarte A, Genz M, Skalden L, Nobili A, Vickers C, Melse O, Kuipers R, Joosten HJ, Stourac J, Bendl J, Black J, Haase P, Baakman C, Damborsky J, Bornscheuer U, Vriend G, Venselaar H.

Protein Eng Des Sel. 2017 May 5:1-7. doi: 10.1093/protein/gzx024. [Epub ahead of print]

PMID:
28475759
4.

GPCRdb: an information system for G protein-coupled receptors.

Isberg V, Mordalski S, Munk C, Rataj K, Harpsøe K, Hauser AS, Vroling B, Bojarski AJ, Vriend G, Gloriam DE.

Nucleic Acids Res. 2017 Mar 17;45(5):2936. doi: 10.1093/nar/gkw1218. No abstract available.

5.

Validation and correction of Zn-CysxHisy complexes.

Touw WG, van Beusekom B, Evers JM, Vriend G, Joosten RP.

Acta Crystallogr D Struct Biol. 2016 Oct 1;72(Pt 10):1110-1118. Epub 2016 Sep 15.

6.

The role of the dopamine D1 receptor in social cognition: studies using a novel genetic rat model.

Homberg JR, Olivier JD, VandenBroeke M, Youn J, Ellenbroek AK, Karel P, Shan L, van Boxtel R, Ooms S, Balemans M, Langedijk J, Muller M, Vriend G, Cools AR, Cuppen E, Ellenbroek BA.

Dis Model Mech. 2016 Oct 1;9(10):1147-1158. Epub 2016 May 19.

7.
8.

New Biological Insights from Better Structure Models.

Touw WG, Joosten RP, Vriend G.

J Mol Biol. 2016 Mar 27;428(6):1375-93. doi: 10.1016/j.jmb.2016.02.002. Epub 2016 Feb 8. Review.

9.

GPCRdb: an information system for G protein-coupled receptors.

Isberg V, Mordalski S, Munk C, Rataj K, Harpsøe K, Hauser AS, Vroling B, Bojarski AJ, Vriend G, Gloriam DE.

Nucleic Acids Res. 2016 Jan 4;44(D1):D356-64. doi: 10.1093/nar/gkv1178. Epub 2015 Nov 17. Erratum in: Nucleic Acids Res. 2016 Dec 6;:.

10.

KMAD: knowledge-based multiple sequence alignment for intrinsically disordered proteins.

Lange J, Wyrwicz LS, Vriend G.

Bioinformatics. 2016 Mar 15;32(6):932-6. doi: 10.1093/bioinformatics/btv663. Epub 2015 Nov 14.

11.

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.

12.

Stabilization of protein-protein interaction complexes through small molecules.

Zarzycka B, Kuenemann MA, Miteva MA, Nicolaes GA, Vriend G, Sperandio O.

Drug Discov Today. 2016 Jan;21(1):48-57. doi: 10.1016/j.drudis.2015.09.011. Epub 2015 Oct 3. Review.

PMID:
26434617
13.

iPPI-DB: an online database of modulators of protein-protein interactions.

Labbé CM, Kuenemann MA, Zarzycka B, Vriend G, Nicolaes GA, Lagorce D, Miteva MA, Villoutreix BO, Sperandio O.

Nucleic Acids Res. 2016 Jan 4;44(D1):D542-7. doi: 10.1093/nar/gkv982. Epub 2015 Oct 1.

14.

Detection of trans-cis flips and peptide-plane flips in protein structures.

Touw WG, Joosten RP, Vriend G.

Acta Crystallogr D Biol Crystallogr. 2015 Aug;71(Pt 8):1604-14. doi: 10.1107/S1399004715008263. Epub 2015 Jul 28.

15.

Quantum chemical study of the isomerization of 24-methylenecycloartanol, a potential marker of olive oil refining.

Wedler HB, Pemberton RP, Lounnas V, Vriend G, Tantillo DJ, Wang SC.

J Mol Model. 2015 May;21(5):111. doi: 10.1007/s00894-015-2652-y. Epub 2015 Apr 10.

PMID:
25860110
16.

New ways to boost molecular dynamics simulations.

Krieger E, Vriend G.

J Comput Chem. 2015 May 15;36(13):996-1007. doi: 10.1002/jcc.23899. Epub 2015 Mar 30.

17.

Key challenges for the creation and maintenance of specialist protein resources.

Holliday GL, Bairoch A, Bagos PG, Chatonnet A, Craik DJ, Finn RD, Henrissat B, Landsman D, Manning G, Nagano N, O'Donovan C, Pruitt KD, Rawlings ND, Saier M, Sowdhamini R, Spedding M, Srinivasan N, Vriend G, Babbitt PC, Bateman A.

Proteins. 2015 Jun;83(6):1005-13. doi: 10.1002/prot.24803. Epub 2015 Apr 22.

18.

Discovery of small molecule CD40-TRAF6 inhibitors.

Zarzycka B, Seijkens T, Nabuurs SB, Ritschel T, Grommes J, Soehnlein O, Schrijver R, van Tiel CM, Hackeng TM, Weber C, Giehler F, Kieser A, Lutgens E, Vriend G, Nicolaes GA.

J Chem Inf Model. 2015 Feb 23;55(2):294-307. doi: 10.1021/ci500631e. Epub 2015 Jan 27.

PMID:
25622654
19.

A series of PDB-related databanks for everyday needs.

Touw WG, Baakman C, Black J, te Beek TA, Krieger E, Joosten RP, Vriend G.

Nucleic Acids Res. 2015 Jan;43(Database issue):D364-8. doi: 10.1093/nar/gku1028. Epub 2014 Oct 28.

20.

BDB: databank of PDB files with consistent B-factors.

Touw WG, Vriend G.

Protein Eng Des Sel. 2014 Nov;27(11):457-62. doi: 10.1093/protein/gzu044.

PMID:
25336027

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