Publications in international journals 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. , 2002 , PDF


  • Dandekar T, Snel B, Schmidt S, Lathe W, Suyama M, Huynen M, Bork P.
    Comparative Genome Analysis of the Mollicutes.
    Molecular Biology and Pathogenity of Mycoplasmas , Edited by Razin and Herrmann, Kluwer Academic/Plenum Publishers, New York, 255-278., 2002 , PDF


  • Duijf PH, Vanmolkot KR, Propping P, Friedl W, Krieger E, McKeon F, Dotsch V, Brunner HG, van Bokhoven H.
    Gain-of-function mutation in ADULT syndrome reveals the presence of a second transactivation domain in p63.
    Hum Mol Genet, Apr 1;11(7):799-804., 2002 , PDF


  • Fernandez M, Kleerebezem M, Kuipers OP, Siezen RJ, van Kranenburg R.
    Regulation of the metC-cysK operon, involved in sulfur metabolism in Lactococcus lactis.
    J Bacteriol , Jan;184(1):82-90., 2002 , PDF


  • Flohil JA, Vriend G, Berendsen HJ.
    Completion and refinement of 3-D homology models with restricted molecular dynamics: application to targets 47, 58, and 111 in the CASP modeling competition and posterior analysis.
    Proteins, Sep 1;48(4):593-604., 2002 , PDF


  • Geijtenbeek TB, van Duijnhoven GC, van Vliet SJ, Krieger E, Vriend G, Figdor CG, van Kooyk Y.
    Identification of different binding sites in the dendritic cell-specific receptor DC-SIGN fpor ICAM-3 and HIV-1.
    J Biol Chem, Mar 29;277(13):11314-11320., 2002 , PDF


  • Hackstein JH, van Hoek AH, Leunissen JA, Huynen M.
    Anaerobic ciliates and their methanogenic endosymbionts.
    Symbiosis: Mechanisms and Model Systems, Edited by J. Seckbach, Kluwer, Dordrecht, The Netherlands, 451-464., 2002 , PDF


  • Kappé G, Leunissen JA, de Jong WW.
    Evolution and diversity of prokaryotic small heat shock proteins.
    Prog Mol Subcell Biol, 28:1-17., 2002 , PDF


  • Klaenhammer T, Altermann E, Arigoni F, Bolotin A, Breidt F, Broadbent J, Cano R, Chaillou S, Deutscher J, Gasson M, van de Guchte M, Guzzo J, Hartke A, Hawkins T, Hols P, Hutkins R, Kleerebezem M, Kok J, Kuipers O, Lubbers M, Maguin E, McKay L, Mills D, Nauta A, Overbeek R, Pel H, Pridmore D, Saier M, van Sinderen D, Sorokin A, Steele J, O’Sullivan D, de Vos W, Weimer B, Zagorec M, Siezen R.
    Discovering lactic acid bacteria by genomics.
    Antonie van Leeuwenhoek , Aug;82(1-4):29-58., 2002 , PDF


  • Klevering BJ, van Driel M, van Hogerwou AJ, van De Pol DJ, Deutman AF, Pinckers AJ, Cremers FP, Hoyng CB.
    Central areolar choroidal dystrophy associated with dominantly inherited drusen.
    Br J Ophthalmol, Jan;86(1):91-6., 2002 , PDF


  • Kloks CP, Spronk CA, Lasonder E, Hoffmann A, Vuister GW, Grzesiek S, Hilbers CW.
    The solution structure and DNA binding properties of the cold shock domain of the human Y-box protein YB-1.
    J Mol Biol, Feb 15;316(2):317-326., 2002 , PDF


  • Kluskens LD, Voorhorst WG, Siezen RJ, Schwerdtfeger RM, Antranikian G, Van Der Oost J, De Vos WM.
    Molecular characterization of fervidolysin, a subtilisin-like serine protease from the thermophilic bacterium Fervidobacterium pennivorans.
    Extremophiles, Jun;6(3):185-194., 2002 , PDF


  • Korbel J, Snel B, Huynen MA, Bork P.
    SHOT: a web server for the construction of genome phylogenies.
    Trends in Genetics, Mar;18(3):158-162., 2002 , PDF


  • van Kranenburg R, Kleerebezem M, van Hylckama Vlieg J, Ursing BM, Smit BA, Ayad E, Smit G, Siezen RJ.
    Flavour formation from amino acids by lactic acid bacteria: predictions from genome sequence analysis.
    Int. Dairy Journal , 12(2-3), 111-121., 2002 , PDF


  • Krieger E, Koraimann G, Vriend G.
    Increasing the precision of comparative models with YASARA NOVA - a self-parameterizing force field.
    Proteins, May 15;47(3):393-402., 2002 , PDF


  • de Kreij A, van den Burg B, Venema G, Vriend G, Eijsink VG, Nielsen JE.
    The effects of modifying the surface charge on the catalytic activity of a thermolysin-like protease.
    J Biol Chem, May 3;277(18):15432-15438., 2002 , PDF


  • Krieger E, Vriend G.
    Models@Home - distributed computing in bioinformatics using a screensaver based approach.
    Bioinformatics, Feb;18(2):315-318., 2002 , PDF


  • Leunissen JA, van Driel MA, Cuelenaere K, Neerincx P, Degenhart GH, Brunner HG.
    Harvesting biological data using bioinformatics: Prediction of human disease genes.
    Calcif Tissue Int, 70, 246., 2002


  • von Mering C, Krause R, Snel B, Cornell M, Oliver SG, Fields S, Bork P.
    Comparative assessment of large-scale data sets of protein-protein interactions.
    Nature, May 23;417(6887):399-403., 2002 , PDF


  • 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., 2002 , PDF


  • Oliveira L, Paiva AC, Vriend G.
    Correlated mutation analyses on very large sequence families.
    Chembiochem, Oct 4;3(10):1010-1017., 2002 , PDF


  • van der Oost J, Huynen MA, Verhees CH.
    Molecular characterization of phosphoglycerate mutase in archaea.
    FEMS Microbiol Lett , Jun 18;212(1):111-120., 2002 , PDF


  • Schell MA, Karmirantzou M, Snel B, Vilanova D, Berger B, Pessi G, Zwahlen MC, Desiere F, Bork P, Delley M, Pridmore RD, Arigoni F.
    The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract.
    Proc Natl Acad Sci U S A, Oct 29;99(22):14422-14427., 2002 , PDF


  • Schulz HL, Stoehr H, White K, van Driel MA, Hoyng CB, Cremers F, Weber BH.
    Genomic structure and assessment of the retinally expressed RFamide-related peptide gene in dominant cystoid macular dystrophy.
    Molecular Vision , Mar 19;8:67-71., 2002 , PDF


  • Singer MS, Vriend G, Bywater RP.
    Prediction of protein residue contacts with a PDB-derived likelihood matrix.
    Protein Eng, Sep;15(9):721-725., 2002 , PDF


  • Snel B, Bork P, Huynen MA.
    Conservation of gene co-regulation in prokaryotes and eukaryotes.
    Trends Biotechnol, Oct 1;20(10):410., 2002 , PDF


  • Snel B, Bork P, Huynen MA.
    The identification of functional modules from the genomic association of genes.
    Proc Natl Acad Sci U S A, Apr 30;99(9):5890-5895., 2002 , PDF


  • Snel B, Bork P, Huynen MA.
    Genomes in flux: the evolution of archaeal and proteobacterial gene content.
    Genome Research , Jan;12(1):17-25., 2002 , PDF


  • Spronk CA, Linge JP, Hilbers CW, Vuister GW.
    Improving the quality of protein structures determined by NMR spectroscopy.
    J Biomol NMR, Mar;22(3):281-289., 2002 , PDF


  • 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., 2002 , PDF


  • 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., 2002 , PDF


  • Voncken FG, Boxma B, van Hoek AH, Akhmanova AS, Vogels GD, Huynen M, Veenhuis M, Hackstein JH.
    A hydrogenosomal [Fe]-hydrogenase from the anaerobic chytrid Neocallimastix sp. L2.
    Gene, Feb 6;284(1-2):103-112., 2002 , PDF


  • Voncken F, Boxma B, Tjaden J, Akhmanova A, Huynen M, Verbeek F, Tielens AG, Haferkamp I, Neuhaus HE, Vogels G, Veenhuis M, Hackstein JH.
    Multiple origins of hydrogenosomes: A mitochondrial-type ADP/ATP carrier from the hydrogenosomes of the anaerobic chytrid Neocallimastix sp. L2.
    Molecular Microbiology, Jun;44(6):1441-1454., 2002 , PDF


  • Walma T, Spronk CA, Tessari M, Aelen J, Schepens J, Hendriks W, Vuister GW.
    Structure, dynamics and binding characteristics of the second PDZ domain of PTP-BL.
    Journal of Molecular Biology, Mar 8;316(5):1101-1110., 2002 , PDF


  • Siezen RJ.
    Genomics versterkt biotechnologie.
    Interview in Zuivelzicht, 94, 16-17., 2002


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