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Results: 1 to 20 of 46

1.

Data-driven medicinal chemistry in the era of big data.

Lusher SJ, McGuire R, van Schaik RC, Nicholson CD, de Vlieg J.

Drug Discov Today. 2014 Jul;19(7):859-68. doi: 10.1016/j.drudis.2013.12.004. Epub 2013 Dec 17.

PMID:
24361338
[PubMed - in process]
2.

Prednisolone induces the Wnt signalling pathway in 3T3-L1 adipocytes.

Fleuren WW, Linssen MM, Toonen EJ, van der Zon GC, Guigas B, de Vlieg J, Dokter WH, Ouwens DM, Alkema W.

Arch Physiol Biochem. 2013 May;119(2):52-64. doi: 10.3109/13813455.2013.774022. Epub 2013 Mar 19.

PMID:
23506355
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Identification of new biomarker candidates for glucocorticoid induced insulin resistance using literature mining.

Fleuren WW, Toonen EJ, Verhoeven S, Frijters R, Hulsen T, Rullmann T, van Schaik R, de Vlieg J, Alkema W.

BioData Min. 2013 Feb 4;6(1):2. doi: 10.1186/1756-0381-6-2.

PMID:
23379763
[PubMed]
Free PMC Article
4.

Org 214007-0: a novel non-steroidal selective glucocorticoid receptor modulator with full anti-inflammatory properties and improved therapeutic index.

van Lierop MJ, Alkema W, Laskewitz AJ, Dijkema R, van der Maaden HM, Smit MJ, Plate R, Conti PG, Jans CG, Timmers CM, van Boeckel CA, Lusher SJ, McGuire R, van Schaik RC, de Vlieg J, Smeets RL, Hofstra CL, Boots AM, van Duin M, Ingelse BA, Schoonen WG, Grefhorst A, van Dijk TH, Kuipers F, Dokter WH.

PLoS One. 2012;7(11):e48385. doi: 10.1371/journal.pone.0048385. Epub 2012 Nov 12.

PMID:
23152771
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

X-ray structure of p38α bound to TAK-715: comparison with three classic inhibitors.

Azevedo R, van Zeeland M, Raaijmakers H, Kazemier B, de Vlieg J, Oubrie A.

Acta Crystallogr D Biol Crystallogr. 2012 Aug;68(Pt 8):1041-50. doi: 10.1107/S090744491201997X. Epub 2012 Jul 17.

PMID:
22868770
[PubMed - indexed for MEDLINE]
6.

Pharmacophore fingerprint-based approach to binding site subpocket similarity and its application to bioisostere replacement.

Wood DJ, de Vlieg J, Wagener M, Ritschel T.

J Chem Inf Model. 2012 Aug 27;52(8):2031-43. doi: 10.1021/ci3000776. Epub 2012 Aug 16.

PMID:
22830492
[PubMed - indexed for MEDLINE]
7.

Comparative analysis of pharmacophore screening tools.

Sanders MP, Barbosa AJ, Zarzycka B, Nicolaes GA, Klomp JP, de Vlieg J, Del Rio A.

J Chem Inf Model. 2012 Jun 25;52(6):1607-20. doi: 10.1021/ci2005274. Epub 2012 Jun 13.

PMID:
22646988
[PubMed - indexed for MEDLINE]
8.

Integrated project views: decision support platform for drug discovery project teams.

Baede EJ, den Bekker E, Boiten JW, Cronin D, van Gammeren R, de Vlieg J.

J Chem Inf Model. 2012 Jun 25;52(6):1438-49. doi: 10.1021/ci200253g. Epub 2012 Jun 13.

PMID:
22640375
[PubMed - indexed for MEDLINE]
9.

A prospective cross-screening study on G-protein-coupled receptors: lessons learned in virtual compound library design.

Sanders MP, Roumen L, van der Horst E, Lane JR, Vischer HF, van Offenbeek J, de Vries H, Verhoeven S, Chow KY, Verkaar F, Beukers MW, McGuire R, Leurs R, Ijzerman AP, de Vlieg J, de Esch IJ, Zaman GJ, Klomp JP, Bender A, de Graaf C.

J Med Chem. 2012 Jun 14;55(11):5311-25. doi: 10.1021/jm300280e. Epub 2012 May 23.

PMID:
22563707
[PubMed - indexed for MEDLINE]
10.

X-ray structures of progesterone receptor ligand binding domain in its agonist state reveal differing mechanisms for mixed profiles of 11β-substituted steroids.

Lusher SJ, Raaijmakers HC, Vu-Pham D, Kazemier B, Bosch R, McGuire R, Azevedo R, Hamersma H, Dechering K, Oubrie A, van Duin M, de Vlieg J.

J Biol Chem. 2012 Jun 8;287(24):20333-43. doi: 10.1074/jbc.M111.308403. Epub 2012 Apr 25.

PMID:
22535964
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Quantum mechanical polar surface area.

Schaftenaar G, de Vlieg J.

J Comput Aided Mol Des. 2012 Mar;26(3):311-8. doi: 10.1007/s10822-012-9557-y. Epub 2012 Mar 4.

PMID:
22391921
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Revisiting the rule of five on the basis of pharmacokinetic data from rat.

Ridder L, Wang H, de Vlieg J, Wagener M.

ChemMedChem. 2011 Nov 4;6(11):1967-70. doi: 10.1002/cmdc.201100306. Epub 2011 Sep 20. No abstract available.

PMID:
21932224
[PubMed - indexed for MEDLINE]
13.

Snooker: a structure-based pharmacophore generation tool applied to class A GPCRs.

Sanders MP, Verhoeven S, de Graaf C, Roumen L, Vroling B, Nabuurs SB, de Vlieg J, Klomp JP.

J Chem Inf Model. 2011 Sep 26;51(9):2277-92. doi: 10.1021/ci200088d. Epub 2011 Sep 6.

PMID:
21866955
[PubMed - indexed for MEDLINE]
14.

Structural basis for agonism and antagonism for a set of chemically related progesterone receptor modulators.

Lusher SJ, Raaijmakers HC, Vu-Pham D, Dechering K, Lam TW, Brown AR, Hamilton NM, Nimz O, Bosch R, McGuire R, Oubrie A, de Vlieg J.

J Biol Chem. 2011 Oct 7;286(40):35079-86. doi: 10.1074/jbc.M111.273029. Epub 2011 Aug 17.

PMID:
21849509
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

ss-TEA: Entropy based identification of receptor specific ligand binding residues from a multiple sequence alignment of class A GPCRs.

Sanders MP, Fleuren WW, Verhoeven S, van den Beld S, Alkema W, de Vlieg J, Klomp JP.

BMC Bioinformatics. 2011 Aug 10;12:332. doi: 10.1186/1471-2105-12-332.

PMID:
21831265
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

CoPub update: CoPub 5.0 a text mining system to answer biological questions.

Fleuren WW, Verhoeven S, Frijters R, Heupers B, Polman J, van Schaik R, de Vlieg J, Alkema W.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W450-4. doi: 10.1093/nar/gkr310. Epub 2011 May 27.

PMID:
21622961
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

A molecular informatics view on best practice in multi-parameter compound optimization.

Lusher SJ, McGuire R, Azevedo R, Boiten JW, van Schaik RC, de Vlieg J.

Drug Discov Today. 2011 Jul;16(13-14):555-68. doi: 10.1016/j.drudis.2011.05.005. Epub 2011 May 13. Review.

PMID:
21605698
[PubMed - indexed for MEDLINE]
18.

GPCRDB: information system for G protein-coupled receptors.

Vroling B, Sanders M, Baakman C, Borrmann A, Verhoeven S, Klomp J, Oliveira L, de Vlieg J, Vriend G.

Nucleic Acids Res. 2011 Jan;39(Database issue):D309-19. doi: 10.1093/nar/gkq1009. Epub 2010 Nov 2.

PMID:
21045054
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Literature mining for the discovery of hidden connections between drugs, genes and diseases.

Frijters R, van Vugt M, Smeets R, van Schaik R, de Vlieg J, Alkema W.

PLoS Comput Biol. 2010 Sep 23;6(9). pii: e1000943. doi: 10.1371/journal.pcbi.1000943.

PMID:
20885778
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Prednisolone-induced differential gene expression in mouse liver carrying wild type or a dimerization-defective glucocorticoid receptor.

Frijters R, Fleuren W, Toonen EJ, Tuckermann JP, Reichardt HM, van der Maaden H, van Elsas A, van Lierop MJ, Dokter W, de Vlieg J, Alkema W.

BMC Genomics. 2010 Jun 5;11:359. doi: 10.1186/1471-2164-11-359.

PMID:
20525385
[PubMed - indexed for MEDLINE]
Free PMC Article

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