Data-driven medicinal chemistry in the era of big data

Authors: Lusher, Scott J., McGuire, Ross, van Schaik, René C., Nicholson, C. David, de Vlieg, Jacob

Source: In Drug Discovery Today July 2014 19(7):859-868

X-ray Structures of Progesterone Receptor Ligand Binding Domain in Its Agonist State Reveal Differing Mechanisms for Mixed Profiles of 11β-Substituted Steroids

Authors: Lusher, Scott J., Raaijmakers, Hans C.A., Vu-Pham, Diep, Kazemier, Bert, Bosch, Rolien, McGuire, Ross, Azevedo, Rita, Hamersma, Hans, Dechering, Koen, Oubrie, Arthur, van Duin, Marcel, de Vlieg, Jacob ^**

Source: In Journal of Biological Chemistry 8 June 2012 287(24):20333-20343

Structural Basis for Agonism and Antagonism for a Set of Chemically Related Progesterone Receptor Modulators

Authors: Lusher, Scott J., Raaijmakers, Hans C.A., Vu-Pham, Diep, Dechering, Koen, Lam, Tsang Wai, Brown, Angus R., Hamilton, Niall M., Nimz, Olaf, Bosch, Rolien, McGuire, Ross, Oubrie, Arthur, de Vlieg, Jacob

Source: In Journal of Biological Chemistry 7 October 2011 286(40):35079-35086

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

Authors: Lusher, Scott J., McGuire, Ross, Azevedo, Rita, Boiten, Jan-Willem, van Schaik, Rene C., de Vlieg, Jacob

Source: In Drug Discovery Today 2011 16(13):555-568

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

Authors: Fleuren, Wilco W. M., Linssen, Margot M. L., Toonen, Erik J. M., van der Zon, Gerard C. M., Guigas, Bruno, de Vlieg, Jacob, Dokter, Wim H. A., Ouwens, D. Margriet, Alkema, Wynand

Source: Archives of physiology and biochemistry. 119(2):52-64

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100125407787.0x000001&indx=1&recIds=ETOCvdc_100125407787.0x000001

Comparison between steroid binding to membrane progesterone receptor α (mPRα) and to nuclear progesterone receptor: Correlation with physicochemical properties assessed by comparative molecular field analysis and identification of mPRα-specific agonists

Authors: Kelder, Jan, Azevedo, Rita, Pang, Yefei, de Vlieg, Jacob, Dong, Jing, Thomas, Peter

Source: In Steroids 2010 75(4):314-322

A Family-based Approach Reveals the Function of Residues in the Nuclear Receptor Ligand-binding Domain

Authors: Folkertsma, Simon, van Noort, Paula, Van Durme, Joost, Joosten, Henk-Jan, Bettler, Emmanuel, Fleuren, Wilco, Oliveira, Laerte, Horn, Florence, de Vlieg, Jacob, Vriend, Gerrit ^∗

Source: In Journal of Molecular Biology 6 August 2004 341(2):321-335

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

Authors: Fleuren Wilco WM, Toonen Erik JM, Verhoeven Stefan, Frijters Raoul, Hulsen Tim, Rullmann Ton, van Schaik René, de Vlieg Jacob, Alkema Wynand

Source: BioData Mining, Vol 6, Iss 1, p 2 (2013)

Subject Terms: Literature mining, Insulin resistance, Glucocorticoids, Gene networks, Computer applications to medicine. Medical informatics, R858-859.7, Analysis, QA299.6-433

File Description: electronic resource

Relation: http://www.biodatamining.org/content/6/1/2; https://doaj.org/toc/1756-0381

Access URL: https://doaj.org/article/bc3cec30a13c497c8b3082c2adfe5c69

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

Authors: Alkema Wynand, van den Beld Sven, Verhoeven Stefan, Fleuren Wilco WM, Sanders Marijn PA, de Vlieg Jacob, Klomp Jan PG

Source: BMC Bioinformatics, Vol 12, Iss 1, p 332 (2011)

Subject Terms: Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5

File Description: electronic resource

Relation: http://www.biomedcentral.com/1471-2105/12/332; https://doaj.org/toc/1471-2105

Access URL: https://doaj.org/article/de55150d571a48e894b51cdeafe27af9

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

Authors: Dokter Wim, van Lierop Marie-Jose, van Elsas Andrea, van der Maaden Hans, Reichardt Holger M, Tuckermann Jan P, Toonen Erik JM, Fleuren Wilco, Frijters Raoul, de Vlieg Jacob, Alkema Wynand

Source: BMC Genomics, Vol 11, Iss 1, p 359 (2010)

Subject Terms: Biotechnology, TP248.13-248.65, Genetics, QH426-470

File Description: electronic resource

Relation: http://www.biomedcentral.com/1471-2164/11/359; https://doaj.org/toc/1471-2164

Access URL: https://doaj.org/article/02388087991e4693b3bf9e0863dcb748

Integrating gene expression and GO classification for PCA by preclustering

Authors: Bauerschmidt Susanne, de Vlieg Jacob, van Schaik Rene C, Piek Ester, De Haan Jorn R, Buydens Lutgarde MC, Wehrens Ron

Source: BMC Bioinformatics, Vol 11, Iss 1, p 158 (2010)

Subject Terms: Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5

File Description: electronic resource

Relation: http://www.biomedcentral.com/1471-2105/11/158; https://doaj.org/toc/1471-2105

Access URL: https://doaj.org/article/d3046b1b424a4a86b7c722e438a82557

BioVenn – a web application for the comparison and visualization of biological lists using area-proportional Venn diagrams

Authors: de Vlieg Jacob, Hulsen Tim, Alkema Wynand

Source: BMC Genomics, Vol 9, Iss 1, p 488 (2008)

Subject Terms: Biotechnology, TP248.13-248.65, Genetics, QH426-470

File Description: electronic resource

Relation: http://www.biomedcentral.com/1471-2164/9/488; https://doaj.org/toc/1471-2164

Access URL: https://doaj.org/article/26a0b4e56b6e43a196ec3d506d3afca0

Testing statistical significance scores of sequence comparison methods with structure similarity

Authors: Leunissen Jack AM, de Vlieg Jacob, Hulsen Tim, Groenen Peter MA

Source: BMC Bioinformatics, Vol 7, Iss 1, p 444 (2006)

Subject Terms: Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5

File Description: electronic resource

Relation: http://www.biomedcentral.com/1471-2105/7/444; https://doaj.org/toc/1471-2105

Access URL: https://doaj.org/article/63d097e56305498f8a75765a0961f8da

PhyloPat: phylogenetic pattern analysis of eukaryotic genes

Authors: de Vlieg Jacob, Hulsen Tim, Groenen Peter MA

Source: BMC Bioinformatics, Vol 7, Iss 1, p 398 (2006)

Subject Terms: Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5

File Description: electronic resource

Relation: http://www.biomedcentral.com/1471-2105/7/398; https://doaj.org/toc/1471-2105

Access URL: https://doaj.org/article/47b12c7600cf48cfb103ae901e977ad5

Fusarium solani pisi cutinase

Authors: Egmond, Maarten R ^*, de Vlieg, Jacob

Source: In Biochimie 2000 82(11):1015-1021

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