Publications of the Computational drug discovery group

2012 Lusher SJ, Raaijmakers HC, Vu Pham D, Kazemier B, Bosch R, McGuire R, Azevedo R, Dechering K, Oubrie A, van Duin M, de Vlieg J.
X-ray structures of the progesterone receptor ligand-binding domain in its agonist state reveal differing mechanisms for the mixed profiles of 11β-substituted steroids.
J Biol Chem, Apr 25. [Epub ahead of print] Details

2011 Bruinsma IB, Karawajczyk A, Schaftenaar G, de Waal RMW, Verbeek MM, van Delft FL.
A rational design to create hybrid beta-sheet breaker peptides to inhibit aggregation and toxicity of amyloid-beta.
MedChemComm, 2:60-64. Details

2011 Sanders MPA, Fleuren WWM, Verhoeven S, van den Beld S, Alkema W, de Vlieg J, Klomp JPG.
ss-TEA: Entropy based identification of receptor specific ligand binding residues from a multiple sequence alignment of class A GPCRs.
BMC Bioinformatics, 12:332 Details

2011 Sanders MP, McGuire R, Roumen L, de Esch IJ, de Vlieg J, Klomp JP, de Graaf C.
From the protein's perspective: the benefits and challenges of protein structure-based pharmacophore modeling.
Med Chem Commun, 3:28-38. Details

2011 Noordermeer SM, Sanders MA, Gilissen C, Tönnissen E, van der Heijden A, Döhner K, Bullinger L, Jansen JH, Valk PJ, van der Reijden BA.
High BRE expression predicts favorable outcome in adult acute myeloid leukemia, in particular among MLL-AF9-positive patients.
Blood, Nov 17;118(20):5613-5621. Details

2011 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.
Structural basis for agonism and antagonism for a set of chemically related progesterone receptor modulators.
J Biol Chem, Oct 7;286(40):35079-35086. Details

2011 Lusher SJ, Conti P, Dokter W, Hermkens PH, De Vlieg J.
Drug design approaches to manipulate the agonist-antagonist equilibrium in steroid receptor modulators.
Steroid Hormones, 221-234. Details

2011 Lusher SJ, McGuire R, Azevedo R, Boiten JW, van Schaik RC, de Vlieg J.
A molecular informatics view on best practice in multi-parameter compound optimization.
Drug Discov Today, Jul;16(13-14):555-568. Details

2010 de Brouwer AP, van Bokhoven H, Nabuurs SB, Arts WF, Christodoulou J, Duley J.
PRPS1 mutations: four distinct syndromes and potential treatment.
Am J Hum Genet, Apr 9;86(4):506-518. Details

2010 Snelders E, Karawajczyk A, Schaftenaar G, Verweij PE, Melchers WJ.
Azole Resistance Profile of Amino Acid Changes in Aspergillus fumigatus CYP51A Based on Protein Homology Modeling.
Antimicrob. Agents Chemother, 54:2425-2430. Details

2010 Frijters R, van Vugt M, Smeets R, van Schaik R, de Vlieg J, Alkema W.
Literature mining for the discovery of hidden connections between drugs, genes and diseases.
PLoS Comput Biol, Sep 23;6(9):e1000943. Details

2010 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.
Prednisolone-induced differential gene expression in mouse liver carrying wild type or a dimerization-defective glucocorticoid receptor.
BMC Genomics, Jun 5;11:359. Details

2010 Venselaar H, Te Beek TA, Kuipers RK, Hekkelman ML, Vriend G.
Protein structure analysis of mutations causing inheritable diseases. An e-Science approach with life scientist friendly interfaces.
BMC Bioinformatics, Nov 8;11(1):548. Details

2009 Thiadens AA, den Hollander AI, Roosing S, Nabuurs SB, Zekveld-Vroon RC, Collin RW, De Baere E, Koenekoop RK, van Schooneveld MJ, Strom TM, van Lith-Verhoeven JJ, Lotery AJ, van Moll-Ramirez N, Leroy BP, van den Born LI, Hoyng CB, Cremers FP, Klaver CC.
Homozygosity mapping reveals PDE6C mutations in patients with early-onset cone photoreceptor disorders.
Am J Hum Genet, Aug;85(2):240-247. Details

2009 Gorissen M, Bernier NJ, Nabuurs SB, Flik G, Huising MO.
Two divergent leptin paralogues in zebrafish (Danio rerio) that originate early in teleostean evolution.
J Endocrinol, Jun;201(3):329-339. Details

2009 Vaz B, Möcklinghoff S, Folkertsma S, Lusher S, de Vlieg J, Brunsveld L.
Computational design, synthesis, and evaluation of miniproteins as androgen receptor coactivator mimics.
Chem Commun (Camb), Sep 28;(36):5377-5379. Details

2009 De Pont JJ, Swarts HG, Karawajczyk A, Schaftenaar G, Willems PH, Koenderink JB.
The non-gastric H,K-ATPase as a tool to study the ouabain-binding site in Na,K-ATPase.
Pflugers Arch, Jan;457(3):623-634. Details

2008 Stolte EH, Nabuurs SB, Bury NR, Sturm A, Flik G, Savelkoul HF, Lidy Verburg-van Kemenade BM.
Stress and innate immunity in carp: Corticosteroid receptors and pro-inflammatory cytokines.
Mol Immunol, Nov;46(1):70-79. Details

2008 Boon CJ, Klevering BJ, Hoyng CB, Zonneveld-Vrieling MN, Nabuurs SB, Blokland E, Cremers FP, den Hollander AI.
Basal laminar drusen caused by compound heterozygous variants in the CFH gene.
Am J Hum Genet, Feb;82(2):516-523. Details

2008 Hulsen T, de Vlieg J, Alkema W.
BioVenn - a web application for the comparison and visualization of biological lists using area-proportional Venn diagrams.
BMC Genomics, Oct 16;9(1):488. Details

2008 Hulsen T, Groenen PM, de Vlieg J, Alkema W.
PhyloPat: an updated version of the phylogenetic pattern database contains gene neighborhood.
Nucleic Acids Res, 37(Database issue):D731-737. Details

2008 Frijters R, Heupers B, van Beek P, Bouwhuis M, van Schaik R, de Vlieg J, Polman J, Alkema W.
CoPub: a literature-based keyword enrichment tool for microarray data analysis.
Nucleic Acids Res, 36(Web Server issue):W406-410. Details

2008 Buchanan G, Maillard J, Nabuurs SB, Richardson DJ, Palmer T, Sargent F.
Features of a twin-arginine signal peptide required for recognition by a Tat proofreading chaperone.
FEBS Lett, Dec 10;582(29):3979-3984. Details

2007 Denissov S, van Driel M, Voit R, Hekkelman M, Hulsen T, Hernandez N, Grummt I, Wehrens R, Stunnenberg H.
Identification of novel functional TBP-binding sites and general factor repertoires.
The Embo Journal, Feb 21;26(4):944-954. Details

2007 de Brouwer AP, Williams KL, Duley JA, van Kuilenburg AB, Nabuurs SB, Egmont-Petersen M, Lugtenberg D, Zoetekouw L, Banning MJ, Roeffen M, Hamel BC, Weaving L, Ouvrier RA, Donald JA, Wevers RA, Christodoulou J, van Bokhoven H.
Arts syndrome is caused by loss-of-function mutations in PRPS1.
Am J Hum Genet, Sep;81(3):507-518. Details

2007 Axmann IM, Holtzendorff J, Voss B, Kensche P, Hess WR.
Two distinct types of 6S RNA in Prochlorococcus.
Gene, Dec 30;406(1-2):69-78. Details

2007 Boon CJ, Klevering BJ, Hoyng CB, Zonneveld-Vrieling MN, Nabuurs SB, Blokland E, Cremers FP, den Hollander AI.
Basal laminar drusen caused by compound heterozygous variants in the CFH gene.
American Journal of Human Genetics, Feb;82(2):516-523. Details

2007 Frijters R, Verhoeven S, Alkema W, van Schaik R, Polman J.
Literature-based compound profiling: application to toxicogenomics.
Pharmacogenomics, Nov;8(11):1521-1534. Details

2007 Nabuurs SB, Wagener M, de Vlieg J.
A Flexible Approach to Induced Fit Docking.
J Med Chem, Dec 27;50(26):6507-6518. Details

2007 Vrins C, Vink E, Vandenberghe KE, Frijters R, Seppen J, Groen AK.
The sterol transporting heterodimer ABCG5/ABCG8 requires bile salts to mediate cholesterol efflux.
FEBS Lett, Oct 2;581(24):4616-4620. Details

2006 Giese TJ, Gregersen BA, Liu Y, Nam K, Mayaan E, Moser A, Range K, Faza ON, Lopez CS, Lera AR, Schaftenaar G, Lopez X, Lee TS, Karypis G, York DM.
QCRNA 1.0: A database of quantum calculations for RNA catalysis.
J Mol Graph Model, Dec;25(4):423-433. Details

2006 Huising MO, van Schijndel JE, Kruiswijk CP, Nabuurs SB, Savelkoul HF, Flik G, Verburg-van Kemenade BM.
The presence of multiple and differentially regulated interleukin-12p40 genes in bony fishes signifies an expansion of the vertebrate heterodimeric cytokine family.
Mol Immunol, Apr;43(10):1519-1533. Details

2006 Hulsen T, Huynen MA, de Vlieg J, Groenen PM.
Benchmarking ortholog identification methods using functional genomics data.
Genome Biol, 7(4):R31. Details

2006 Hulsen T, de Vlieg J, Groenen PM.
PhyloPat: phylogenetic pattern analysis of eukaryotic genes.
BMC Bioinformatics, Sep 1;7:398. Details

2006 Hulsen T, de Vlieg J, Leunissen JA, Groenen PM.
Testing statistical significance scores of sequence comparison methods with structure similarity.
BMC Bioinformatics, Oct 12;7:444. Details

2006 Folkertsma S.
The Nuclear Receptor Ligand-Binding Domain: from Biological Function to Drug Design.
PhD Thesis, Details

2006 Huising MO, Geven EJW, Kruiswijk CP, Nabuurs SB, Stolte EH, Spanings FAT, Verburg-van Kemenade BML, Flik G.
Increased leptin expression in common Carp (Cyprinus carpio) after food intake but not after fasting or feeding to satiation.
Endocrinology, Dec;147(12):5786-5797. Details

2005 Folkertsma S, van Noort PI, Brandt RF, Bettler E, Vriend G, de Vlieg J.
The nuclear receptor ligand-binding domain: a family-based structure analysis.
Curr Med Chem, 12(9):1001-1016. Details

2005 Schaftenaar G, de Wijs GA, Sanchez-Portal D, Vlieg E.
Quantum mechanics calculations on the diastereomeric salts of cyclic phosphoric acids with ephedrine.
Journal of Molecular Structure-Theochem, 717:205-214 Details

2004 Borkent JH.
Cheminformatics and chemistry teaching.
Cheminformatics Developments, 1(1):203-217 . Details

2004 Folkertsma S, van Noort P, Van Durme J, Joosten HJ, Bettler E, Fleuren W, Oliveira L, Horn F, de Vlieg J, Vriend G.
A family-based approach reveals the function of residues in the nuclear receptor ligand-binding domain.
J Mol Biol, Aug 6;341(2):321-335. Details

2004 Verwer P, Leusen FJJ.
Cheminformatics and molecular modeling.
Cheminformatics Developments, 175-202. Details

2004 Ott MA.
Cheminformatics and organic chemistry. Computer-assisted synthetic analysis.
Cheminformatics Developments, 1(1-2):83-109. Details

2003 Borkent H, Smith P.
Nieuwe Spectroscopie-webmodule.
NVOX, Nov;9:414-415. Details

2003 Borkent H, van Rooij J, Stueker O, Brunberg I, Fels G.
Mol4D: A Web-Based Computational Chemistry Interface for Educational Purposes.
J Chem Educ, 80(5):582. Details

2003 Stueker O, Brunberg I, Fels G, Borkent H, van Rooij J.
Web-Based Interactive Animation of Organic Reactions.
J Chem Educ, 80(5):583. Details

2002 Boerrigter SX, van den Hoogenhof CJ, Meekes H, Verwer P, Bennema P.
Pseudomorphic Crystal Growth of the Model Steroid Methyl Analogue of Norethindrone.
J Phys Chem B, 106(51):13224-13230. Details

2002 Motherwell WD, Ammon HL, Dunitz JD, Dzyabchenko A, Erk P, Gavezzotti A, Hofmann DW, Leusen FJ, Lommerse JP, Mooij WT, Price SL, Scheraga H, Schweizer B, Schmidt MU, van Eijck BP, Verwer P, Williams DE.
Crystal structure prediction of small organic molecules: a second blind test.
Acta Crystallogr B, Aug;58(Pt 4):647-661. Details

2002 van de Streek J, Verwer P, Bennema P, Vlieg E.
On the influence of thermal motion on the crystal structures and polymorphism of even n-alkanes.
Acta Crystallogr B, Aug;58(Pt 4):677-683. Details

2002 van de Streek J, Verwer P, Bennema P, Vlieg E.
On the irrelevance of electrostatics for the crystal structures and polymorphism of long even n-alkanes.
J Comput Chem, Feb;23(3):365-370. Details

2002 Schaftenaar G.
Computational Chemistry Methods. Applications to Racemate Resolution and Radical Cation Chemistry.
PhD thesis, University of Nijmegen. Details

2001 Habraken CL, Buijs W, Borkent H, Ligeon W, Wenders H, Meijer M.
School Chemistry vs. Chemistry in Research: An Exploratory Experiment.
Journal of Science Education and Technology, 10(3):249-256. Details

2000 Derksen AJ, van der Waals AC, van Ham MH, van Dongen M, Borkent JH, de Gelder R, Klunder AJ, Zwanenburg B.
Unique formation of oxapentacycloundecanones by catalytic flash vacuum thermolysis of tricyclo[5.2.1.0(2,6)]decenone epoxides using mineral solid acids.
Tetrahedron Letters, 41(47):9189-9193. Details

2000 Lommerse JP, Motherwell WD, Ammon HL, Dunitz JD, Gavezzotti A, Hofmann DW, Leusen FJ, Mooij WT, Price SL, Schweizer B, Schmidt MU, van Eijck BP, Verwer P, Williams DE.
A test of crystal structure prediction of small organic molecules.
Acta Crystallogr B, Aug;56(Pt 4):697-714. Details

2000 Schaftenaar G, Noordik JH.
The effect of isodensity surface sampling on ESP derived charges and the effect of adding bondcenters on DMA derived charges.
J Comput Aided Mol Des, Mar;14(3):233-242. Details

2000 Schaftenaar G, Noordik JH.
MOLDEN: a pre- and post-processing program for molecular and electronic structures.
J Comput Aided Mol Des, Feb;14(2):123-134. Details

2000 van de Streek J, Verwer P, de Gelder R, Hollander F.
New evidence for β'-2 p.p+2.p triacylglycerol crystal structure.
J Am Oil Chem Soc, 77(2):215-216. Details

1999 van de Streek J, Verwer P, de Gelder R, Hollander F.
Structural Analogy between β'-Triacylglycerols and n-alkanes. Towards the crystal structure of β'-2 p.p+2.p triacylglycerols.
J Am Oil Chem, 76(11):1333-1341. Details

1999 Leusen FJ, Wilke S, Verwer P, Engel G.
Computational Approaches to Crystal Structure and Polymorph Prediction.
Implications of Molecular and Materials Structure for New Technologies, Edited by Howard JAK, Allen FH, Shields GP. Kluwer Academic Publishers, Dordrecht, pp 303-314.

1999 Hollander FF, Boerrigter SX, van de Streek J, Grimbergen RF, Meekes H, Bennema P.
The implication of the connected net topology on the morphology of β'-monoacid triacylglycerol crystals.
J Phys Chem B, 103(39):8301-8309. Details

1999 Hollander FFA, van de Streek J, Boerrigter SXM, Plomp M, Meekes H, van Enckevort W, Bennema P.
Morphology of β'-2 n.n.n. triacylglycerol crystals: revised interpretation based on the topology of connected nets.
in proceedings of the 14th international symposium on industrial crystallisation, Cambridge, U.K., Sept 12-16, pp 2334-2343.

1999 Nielsen JE, Beier L, Otzen D, Borchert TV, Frantzen HB, Andersen KV, Svendsen A.
Electrostatics in the active site of an alpha-amylase.
Eur J Biochem, Sep;264(3):816-824. Details