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Issue Date	Title	Author(s)
2012	From the proteins perspective: the benefits and challenges of protein structure-based pharmacophore modeling	Sanders, M.P.A.; McGuire, R.; Roumen, L.; de Esch, I.J.; Vlieg, J. de; Klomp, J.P.G.; de Graaf, C.
2012	Flexible protein-ligand docking using the fleksy protocol	Wagener, M.; Vlieg, J. de; Nabuurs, S.B.
2012	Snooker: A structure-based pharmacophore generation tool applied to class a gpcrs	Sanders, M.P.A.; Verhoeven, S.; Graaf, C. de; Roumen, L.; Vroling, B.; Nabuurs, S.B.; Vlieg, J. de; Klomp, J.P.G.
2012	Quantum mechanical polar surface area.	Schaftenaar, G.; Vlieg, J. de
2012	X-ray structures of progesterone receptor ligand binding domain in its agonist state reveal differing mechanisms for mixed profiles of 11beta-substituted steroids.	Lusher, S.J.; Raaijmakers, H.C.A.; Vu-Pham, D.; Kazemier, B.; Bosch, R.; McGuire, R.; Azevedo, R.; Hamersma, H.; Dechering, K.; Oubrie, A.; Duin, M. van; Vlieg, J. de
2012	X-ray structure of p38alpha bound to TAK-715: comparison with three classic inhibitors.	Azevedo, R.; Zeeland, M. van; Raaijmakers, H.; Kazemier, B.; Vlieg, J. de; Oubrie, A.
2012	Integrated project views: decision support platform for drug discovery project teams.	Baede, E.J.; Bekker, E. den; Boiten, J.W.; Cronin, D.; Gammeren, R. van; Vlieg, J. de
2012	Pharmacophore fingerprint-based approach to binding site subpocket similarity and its application to bioisostere replacement	Wood, D.J.; de Vlieg, J.; Wagener, M.; Ritschel, T.
2012	A prospective cross-screening study on G-protein-coupled receptors: lessons learned in virtual compound library design.	Sanders, M.P.A.; Roumen, L.; Horst, E. van der; Lane, J.R.; Vischer, H.F.; Offenbeek, J. van; Vries, H. de; Verhoeven, S.; Chow, K.Y.; Verkaar, F.; Beukers, M.W.; McGuire, R.; Leurs, R.; IJzerman, A.P.; Vlieg, J. de; Esch, I.J. de; Zaman, G.J.; Klomp, J.P.G.; Bender, A.; Graaf, C. de
2012	Comparative analysis of pharmacophore screening tools.	Sanders, M.P.A.; Barbosa, A.J.; Zarzycka, B.; Nicolaes, G.A.; Klomp, J.P.G.; Vlieg, J. de; Rio, A. Del
2012	Org 214007-0: a novel non-steroidal selective glucocorticoid receptor modulator with full anti-inflammatory properties and improved therapeutic index	Lierop, M.J.C. van; Alkema, W.; Laskewitz, A.J.; Dijkema, R.; van der Maaden, H.M.; Smit, M.J.; Plate, R.; Conti, P.G.; Jans, C.G.; Timmers, C.M.; van Boeckel, C.A.; Lusher, S.J.; McGuire, R.; van Schaik, R.C.; de Vlieg, J.; Smeets, R.L.; Hofstra, C.L.; Boots, A.M.H.; van Duin, M.; Ingelse, B.A.; Schoonen, W.G.; Grefhorst, A.; van Dijk, T.H.; Kuipers, F.; Dokter, W.H.
2011	A molecular informatics view on best practice in multi-parameter compound optimization	Lusher, S.J.; McGuire, R.; Azevedo, R.; Boiten, J.W.; Schaik, R.C. Van; Vlieg, J. de
2011	Revisiting the rule of five on the basis of pharmacokinetic data from rat	Ridder, L.; Wang, H.W.; Vlieg, J. de; Wagener, M.
2011	Copub update : Copub 5.0 a text mining system to answer biological questions	Fleuren, W.W.M.; Verhoeven, S.; Frijters, R.J.J.M.; Heupers, B.; Polman, J.; Schaik, R. van; Vlieg, J. de; Alkema, W.
2011	ss-TEA: Entropy based identification of receptor specific ligand binding residues from a multiple sequence alignment of class A GPCRs.	Sanders, M.P.A.; Fleuren, W.W.M.; Verhoeven, S.; Beld, S. van den; Alkema, W.; Vlieg, J. de; Klomp, J.P.G.
2011	Structural basis for agonism and antagonism for a set of chemically related progesterone receptor modulators	Lusher, S.J.; Raaijmakers, H.C.A.; Vu-Pham, D.; Dechering, K.J.; Lam, T.W.; Brown, A.R.; Hamilton, N.M.; Nimz, O.; Bosch, R.; McGuire, R.; Oubrie, A.; Vlieg, J. de
2011	Snooker: a structure-based pharmacophore generation tool applied to class A GPCRs.	Sanders, M.P.A.; Verhoeven, S.; Graaf, C. de; Roumen, L.; Vroling, B.; Nabuurs, S.B.; Vlieg, J. de; Klomp, J.P.G.
2011	Copub update: Copub 5.0 a text mining system to answer biological questions	Fleuren, W.W.M.; Verhoeven, S.; Frijters, R.; Heupers, B.; Polman, J.; Schaik, R. van; Vlieg, J. de; Alkema, W.
2011	In Silico Veritas: The Pitfalls and Challenges of Predicting GPCR-Ligand Interactions.	Roumen, L.; Sanders, M.P.A.; Vroling, B.; Esch, I.J. de; Vlieg, J. de; Leurs, R.; Klomp, J.P.G.; Nabuurs, S.B.; Graaf, C. de
2011	GPCRDB: information system for G protein-coupled receptors	Vroling, B.; Sanders, M.; Baakman, C.A.B.; Borrmann, A.; Verhoeven, S.; Klomp, J.; Oliveira, L.; Vlieg, J. de; Vriend, G.
2010	Integrating gene expression and go classification for pca by preclustering	Haan, J.R. de; Piek, E.; Schaik, R.C. Van; Vlieg, J. de; Bauerschmidt, S.; Buydens, L.M.C.; Wehrens, H.R.M.J.
2010	Literature mining for the discovery of hidden connections between drugs, genes and diseases.	Frijters, R.J.J.M.; Vugt, M. De; Smeets, R.; Schaik, R. van; Vlieg, J. de; Alkema, W.
2010	Prednisolone-induced differential gene expression in mouse liver carrying wild type or a dimerization-defective glucocorticoid receptor	Frijters, R.J.J.M.; Fleuren, W.W.M.; Toonen, E.J.M.; Tuckermann, J.P.; Reichardt, H.M.; Maaden, H. van der; Elsas, A. van; Lierop, M.J.C. van; Dokter, W.; Vlieg, J. de; Alkema, W.
2009	Computational design, synthesis, and evaluation of miniproteins as androgen receptor coactivator mimics	Vaz, B.; Mocklinghoff, S.; Folkertsma, S.; Lusher, S.; Vlieg, J. de; Brunsveld, L.
2009	PhyloPat: an updated version of the phylogenetic pattern database contains gene neighborhood.	Hulsen, T.; Groenen, P.M.A.; Vlieg, J. de; Alkema, W.
2008	CoPub: a literature-based keyword enrichment tool for microarray data analysis.	Frijters, R.; Heupers, B.; Beek, P van; Bouwhuis, M.; Schaik, R. van; Vlieg, J. de; Polman, J.; Alkema, W.
2008	BioVenn - a web application for the comparison and visualization of biological lists using area-proportional Venn diagrams	Hulsen, T.; Vlieg, J. de; Alkema, W.
2007	The use of in vitro peptide binding profiles and in silico ligand-receptor interaction profiles to describe ligand-induced conformations of the retinoid X receptor alpha ligand-binding domain	Folkertsma, S.; Noort, P.I.; Heer, A.; Carati, P.; Brandt, R.; Visser, A.; Vriend, G.; Vlieg, J. de
2007	A Flexible Approach to Induced Fit Docking	Nabuurs, S.B.; Wagener, M.; Vlieg, J. de
2006	Benchmarking ortholog identification methods using functional genomics data	Hulsen, T.; Huynen, M.A.; Vlieg, J. de; Groenen, P.M.A.
2006	PhyloPat : phylogenetic pattern analysis of eukaryotic genes	Hulsen, T.; Vlieg, J. de; Groenen, P.M.A.
2006	Testing statistical significance scores of sequence comparison methods with structure similarity	Hulsen, T.; Vlieg, J. de; Leunissen, J.A.M.; Groenen, P.M.A.
2006	Benchmarking ortholog identification methods using functional genomics data.	Hulsen, T.; Huynen, M.A.; Vlieg, J. de; Groenen, P.M.
2006	Testing statistical significance scores of sequence comparison methods with structure similarity	Hulsen, T.; Vlieg, J. de; Leunissen, J.A.M.; Groenen, P.M.
2006	PhyloPat: phylogenetic pattern analysis of eukaryotic genes	Hulsen, T.; Vlieg, J. de; Groenen, P.M.
2006	Steroid and G Protein Binding Characteristics of the Seatrout and Human Progestin Membrane Receptor Alpha Subtypes and Their Evolutionary Origins	Thomas, P.; Pang, Y.; Dong, J.; Groenen, P.; Kelder, J.; Vlieg, J. de; Zhu, Y.; Tubbs, C.
2005	The nuclear receptor ligand-binding domain: a family-based structure analysis	Folkertsma, S.; Noort, P.I. van; Brandt, R.F.; Bettler, E.J.M.; Vriend, G.; Vlieg, J. de
2004	A family-based approach reveals the function of residues in the nuclear receptor ligand-binding domain.	Folkertsma, S.; Noort, P. van; Durme, J Van; Joosten, H.J.; Bettler, E.J.M.; Fleuren, W.W.M.; Oliveira, L.; Horn, F.; Vlieg, J. de; Vriend, G.