Publications in international journals before 2000
  • Wang J, Bakkers JM, Galama JM, Bruins Slot HJ, Pilipenko EV, Agol VI, Melchers WJ.
    Structural requirements of the higher order RNA kissing element in the enteroviral 3'UTR.
    Nucleic Acids Res, Jan 15;27(2):485-490., 1999 , PDF


  • Williams JC, Zeelen JP, Neubauer G, Vriend G, Backmann J, Michels PA, Lambeir AM, Wierenga RK.
    Structural and mutagenesis studies of leishmania triosephosphate isomerase: a point mutant can convert a mesophilic enzyme into a superstable enzyme without losing catalytic power.
    Protein Eng, Mar;12(3):243-250., 1999 , PDF


  • Boteva R, Visser AJ, Filippi B, Vriend G, Veenhuis M, van der Klei IJ.
    Conformational transitions accompanying oligomerization of yeast alcohol oxidase, a peroxisomal flavoenzyme.
    Biochemistry, Apr 20;38(16):5034-5044., 1999 , PDF


  • Mansfeld J, Vriend G, Van den Burg B, Eijsink VG, Ulbrich-Hofmann R.
    Probing the unfolding region in a thermolysin-like protease by site-specific immobilization.
    Biochemistry, Jun 29;38(26):8240-8245., 1999 , PDF


  • de Groot BL, Vriend G, Berendsen HJ.
    Conformational changes in the chaperonin GRoEL: New insights into the allosteric mechanism.
    J Mol Biol, Mar 5;286(4):1241-1249., 1999 , PDF


  • 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., 1999 , PDF


  • 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., 1999 , PDF


  • 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


  • Celli J, Duijf P, Hamel BC, Bamshad M, Kramer B, Smits AP, Newbury-Ecob R, Hennekam RC, Van Buggenhout G, van Haeringen A, Woods CG, van Essen AJ, de Waal R, Vriend G, Haber DA, Yang A, McKeon F, Brunner HG, van Bokhoven H.
    Heterozygous Germline mutations in the p53 homolog p63 are the cause of EEC syndrome.
    Cell, Oct 15;99(2):143-153., 1999 , PDF


  • Dorelijers JF, Vriend G, Raves ML, Kaptein R.
    Validation of NMR structures of proteins and nucleic acids: hydrogen geometry and nomenclature.
    Proteins, Nov 15;37(3):404-416., 1999 , PDF


  • Oliveira L, Paiva AC, Vriend G.
    A low resolution model for the interaction of G proteins with G protein-coupled receptors.
    Protein Eng, Dec;12(12):1087-1095., 1999 , PDF


  • Nielsen JE, Andersen KV, Honig B, Hooft RW, Klebe G, Vriend G, Wade RC.
    Improving macromolecular electrostatics calculations.
    Protein Eng, Aug;12(8):657-662., 1999 , PDF


  • 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., 1999 , PDF


  • Rodriguez R, Chinea G, Lopez N, Vriend G.
    Full window stereo.
    J Mol Graph Model, Oct-Dec;17(5-6):310-4, 333., 1999 , PDF


  • Siezen RJ.
    Multi-domain, cell-envelope proteinases of lactic acid bacteria.
    Antonie van Leeuwenhoek , Jul-Nov;76(1-4):139-155., 1999 , PDF


  • van Kraaij C, de Vos WM, Siezen RJ, Kuipers OP.
    Lantibiotics: biosynthesis, mode of action and applications.
    Natural Products Report, Oct;16(5):575-587., 1999 , PDF


  • Hiemstra HS, van Veelen PA, Schloot NC, Geluk A, van Meijgaarden KE, Willemen SJ, Leunissen JA, Benckhuijsen WE, Amons R, de Vries RR, Roep BO, Ottenhoff TH, Drijfhout JW.
    Definition of natural T cell antigens with mimicry epitopes obtained from dedicated synthetic peptide libraries.
    J Immunol, Oct 15;161(8):4078-4082., 1998 , PDF


  • Arends RJ, Vermeer H, Martens GJ, Leunissen JA, Wendelaar Bonga SE, Flik G.
    Cloning and expression of two proopiomelanocortin mRNAs in the common carp (Cyprinus carpio L.).
    Mol Cell Endocrinol, Aug 25;143(1-2):23-31., 1998 , PDF


  • Dechering KJ, Cuelenaere K, Konings RN, Leunissen JA.
    Distinct frequency-distributions of homopolymeric DNA tracts in different genomes.
    Nucleic Acids Res, Sep 1;26(17):4056-4062., 1998 , PDF


  • de Jong WW, Caspers GJ, Leunissen JA.
    Genealogy of the alpha-Crystallin/Small Heat-Shock Protein Superfamily.
    Int J Biol Macromol, May-Jun;22(3-4):151-162., 1998 , PDF


  • Vriend G, Berendsen HJ, van den Burg B, Venema G, Eijsink VG.
    Early steps in the unfolding of thermolysin-like proteases.
    J Biol Chem, Dec 25;273(52):35074-35077., 1998 , PDF


  • Mooij WT, van Eijck BP, Price SL, Verwer P, Kroon J.
    Crystal Structure Predictions for Acetic Acid.
    J Comput Chem, Mar;19(4):459-474., 1998 , PDF


  • Verwer P, Leusen FJ.
    Computer Simulation to Predict Possible Crystal Polymorphs.
    Reviews in Computational Chemistry, 12, Edited by Lipkowitz KB, Boyd, DB., VCH Publishers, New York., 1998 , PDF


  • Leunissen JAM.
    Databanken: de spin in het Web.
    Chemisch Magazine, Interview by Marcel Crok, March 1998, 87-89., 1998


  • Siezen RJ, Leunissen JA.
    Subtilases: The superfamily of subtilisin-like serine proteases.
    Protein Sci, Mar;6(3):501-523., 1997 , PDF


  • Melchers WJG, Hoenderop JGJ, Bruins Slot HJ, Pilipenko EV, Galama JMD
    Kissing of the two predominant hairpin-loops in the Coxsackie B virus 3'UTR is the essential structural feature of the origin of replication required for (-) strand RNA synthesis
    J. Virology, 71, 686-696, 1997 , PDF


  • Ott MA, Noordik JH
    Long-range Strategies in the LHASA Program: The Quinone Diels-Alder Transform
    J. Chem. Inf. Comput. Sci, 37, 98-108, 1997 , PDF


  • Noordik JH, Leunissen JAM, Cuelenaere K
    Network Performance Monitoring in EMBnet
    EMBnet news, Vol. 4. nr. 3, 1997 , PDF


  • Baumgart E, Vanhooren JCT, Fransen M, Marynen P, Puype M, Vandekerckhove J, Leunissen JAM, Fahimi HD, Mannaerts GP, Van Veldhoven PP
    Molecular characterization of the human peroxisomal branched-chain acyl-CoA oxidase: cDNA cloning, chromosomal assignment, tissue distribution, and evidence for the absence of the protein in Zellweger syndrome
    Proc. Natl. Acad. Sci. USA 93, 13748-13753, 1996 , PDF


  • Pilipenko EV, Poperechny KV, Maslova SV, Melchers WJG, Bruins Slot HJ, Agol VI
    Cis-element, oriR, involved in the initiation of (-) strand poliovirus RNA: a quasi-globular multi-domain RNA structure maintained by tertiary ('kissing') interactions
    EMBO J, 15, 5428-5436, 1996 , PDF


  • Kremer H, Kuyt LP, van den Helm B, van Reen M, Leunissen JAM, Hamel BCJ, Jansen C, Mariman ECM, Frants RR, Padberg GW
    Localization of a gene for Mbius syndrome to chromosome 3q by linkage analysis in a Dutch family
    Hum. Mol. Genetics , 9, 1367-1371, 1996 , PDF


  • Lamers AE, Groeneveld D, de Kleijn DPV, Geeraedts FCG, Leunissen JAM, Flik G, Wendelaar Bonga SE, Martens GJM
    Cloning and sequence analysis of a hypothalamic cDNA encoding a D1-like dopamine receptor in Tilapia
    Biochim. Biophys. Acta, Acta 1308, 17-22, 1996 , PDF


  • Caspers G-J, Reinders G-J, Leunissen JAM, Wattel J, de Jong WW
    Protein sequences indicate that turtles branched off from the amniote tree after mammals
    J. Mol. Evol, 42, 580-586, 1996 , PDF


  • Kuiken CL, Lukashov VV, Baan E, Dekker J, Leunissen JAM, Goudsmit J
    Evidence for limited within-person evolution of the V3 domain of the HIV-1 envelope in the Amsterdam population
    AIDS, 10, 31-37, 1996 , PDF


  • Janke RH, Haufe G, Wurthwein E-H, Borkent JH
    Racemization barriers of helicenes: a computational study
    J.Am.Chem.Soc., 118 (25), 6031. in cooperation with a research group at the University of M√ľnster in Germany, 1996


  • Verhaar HJM, Rorije E, Borkent H, Seinen W, Hermens JLM
    Modeling the nucleophilic reactivity of small organochlorine electrophiles: a mechanistically based quantitative structure-activity relationship
    Environ.Toxicol.Chem, 15 (6), 1011, 1996


  • Borkent JH
    Visualizing the racemization of Octahelicene
    (published at the ECCC1), electronic publication, 1996 , PDF


  • Borkent JH
    Chemische informatievoorziening (Internet in de praktijk 7)
    Open, 28(4) 99, 1996


  • Borkent JH
    Chemisch gereedschap op het web
    Chemisch Magazine, April, 146, 1996


  • Ott MA
    Computer Methods in Synthetic Analysis
    Applications to Reaction Retrieval and Synthesis Design, PhD thesis, University of Nijmegen (ISBN 90-9009390-7), 1996


  • Caspers G-J, Leunissen JAM, de Jong WW
    The expanding small heat-shock protein family, and structure predictions of the conserved "alpha-crystallin domain
    J. Mol. Evol, 40, 238-248, 1995 , PDF


  • Hackstein JHP, Mackenstedt U, Mehlhorn H, Meijerink JPP, Schubert H, Leunissen JAM
    Parasitic apicomplexans harbour a chlorophyll a-D1 complex, the potential target for therapeutic triazines
    Parasitology Res, 81, 207-216, 1995


  • Siezen RJ, Leunissen JAM, Shinde U
    Homology analysis of the propeptides of subtilisin-like serine proteases (subtilases)
    Intramolecular chaperones and protein folding, Shinde, M Inouye (eds.) RG Landes Company, Austin, pp. 233-256, 1995


  • Boiten J-W, Ott MA, Noordik JH
    Automated Overlap Analysis of Reaction Databases
    J. Chem. Inf. Comput. Sci, 35, 115-120, 1995 , PDF


  • Rice P, Lopez R, Doelz R, Leunissen J
    EGCG 8.0
    EMBnet news, Vol. 2. nr. 2, 1995 , PDF


  • Boiten J-W
    Computer Methods in Organic Synthesis Design
    New and Improved Algorithms for Data Conversion, Synthesis Planning and 3D Perception, PhD thesis, University of Nijmegen (ISBN 90-9007959-9). , 1995


  • Slobbe R, Poels L, ten Dam G, Boerman O, Nieland L, Leunissen J, Ramaekers F, van Eys G
    Analysis of idiotope structure of ovarian cancer antibodies: Recognition of the same epitope by two monoclonal antibodies differing mainly in their heavy chain variable sequences
    Clin. Exp Immunol, 98, 95-103, 1994 , PDF


  • Burger H, Wagemaker G, Leunissen JAM, Dorssers LCJ
    Molecular evolution of interleukin-3
    . J. Mol. Evol, 39, 255-267, 1994 , PDF


  • Pouwels PH, Leunissen JAM
    Divergence in codon usage of Lactobacillus species
    Nucleic Acids Res, 22, 929-936, 1994 , PDF


  • van Gelder CWM, Leusen FJL, Leunissen JAM, Noordik JH
    A molecular dynamics approach for the generation of complete protein structures from limited coordinate data.
    Proteins: Structure, Function and Genetics, 18, 174-185, 1994 , PDF


  • van Rozendaal ELM, Ott MA, Scheeren HW
    A LHASA analysis of taxol
    Recl. Trav. Chim, Pays-Bas 113, 297-303, 1994


  • Miller TM, Boiten J-W, Ott MA, Noordik JH
    Organic Reaction Database Translation from REACCS to ORAC
    J. Chem. Inf. Comput. Sci, 1994, 34, 653-660, 1994 , PDF


  • Moers FG, Smits JMM, Beurskens PT, Ariaans GJ, Zwanenburg B, Leusen FJJ, Bruggink A
    Crystal and Molecular Structure of the Salt of a benzyl alcolhol and a dioxaphosphirane oxide, C12H29NO5PCl
    J. Chem. Cryst, 24, 179-182, 1994


  • de Jong WW, Leunissen JAM, Wistow GJ
    Eye lens crystallins and the phylogeny of placental orders: evidence for a macroscelid-paenungulate clade?
    Mammal phylogeny; placentals, FS Szalay et al. (eds.) Springer-Verlag New York, Inc., pp. 5-12, 1993


  • van der Vlugt RA, Leunissen J, Goldbach R
    Taxonomic relationships between distinct potato virus Y isolates based on detailed comparisons of the viral coat proteins and 3'-nontranslated regions
    Arch. Virol, 131, 361-375, 1993 , PDF


  • de Jong WW, Leunissen JAM, Voorter CEM
    Evolution of the alpha-crystallin/small heat-shock protein family
    Mol. Biol. Evol, 10, 103-126, 1993 , PDF


  • Boiten JW, Noordik JH, Groen MB
    Cationic Polyene Cyclizations. A Computer Assisted Synthesis Approach
    J. Chem. Inf. Comput. Sci, 33, 727-735, 1993 , PDF


  • Leusen FJJ, Noordik JH, Karfunkel HR
    Racemate Resolution via Crystallization of Diastereomeric Salts: Thermodynamic Considerations and Molecular Mechanics Calculations
    Tetrahedron, 49, 5377-5396, 1993


  • Ephraim MJ, Thiers AHM, Janner A, Janssen T
    Applying Smalltalk-80 and C++ to Crystal Symmetry Analysis
    Structured Programming, 14, 119, 1993


  • Ephraim MJ, Thiers AHM, Janner A, Janssen T
    An Object Oriented Approach towards a Crystal Symmetry Environment
    Comp. Physics Comm., 77, 167, 1993


  • Weijers RN, Mulder J, Lawson C, Leunissen J
    Induction of autoantibodies to human enzymes following viral infection: a biologically relevant hypothesis
    Eur. J. Clin. Chem. Clin. Biochem, 30, 449-454, 1992 , PDF


  • Kolakowski LF Jr, Leunissen JAM, Smith JE
    ProSearch: fast searching of protein sequences with regular expression patterns related to protein structure and function
    BioTechniques, 13, 919-921, 1992 , PDF


  • Roebroek AJM, Creemers JWM, Pauli IGL, Kurzik-Dumke U, Rentrop M, Gateff EAF, Leunissen JAM, Van de Ven WJM
    Cloning and functional expression of Dfurin2, a subtilisin-like proprotein processing enzyme of Drosophila melanogaster with multiple repeats of a cysteine motif
    J. Biol. Chem, 267, 17208-17215, 1992 , PDF


  • Kenter M, Otting N, Anholts J, Leunissen J, Jonker M, Bontrop RE
    Evolutionary relationships among the primate Mhc-DQA1 and DQA2 alleles
    Immunogenetics, 36, 71-78, 1992 , PDF


  • Bruins Slot HJ, Leusen FJJ, van der Haest AD, van Bolhuis F
    Structures of a pair of diastereomeric salts of ephedrine and dichloro-substituted cyclic phosphoric acid
    Acta Cryst, C48, 925, 1992 , PDF


  • Bruins Slot HJ, Leusen FJJ, van der Haest AD, van Bolhuis F
    Structures of a pair of diastereomeric salts of ephedrine and fluoro-substituted cyclic phosphoric acid
    Acta Cryst, C48, 587, 1992 , PDF


  • Bruins Slot HJ, Leusen FJJ, van der Haest AD, van Bolhuis F
    Structures of a pair of diastereomeric salts of ephedrine and fluoro-substituted cyclic phosphoric acid
    Acta Cryst, C48, 372, 1992 , PDF


  • Leusen FJJ, Bruins Slot HJ, Noordik JH, van der Haest AD, Wijnberg HA, Bruggink A
    Towards a rational design of resolving agents. Part IV. Crystal packing analyses and molecular mechanics calculations for five pairs of diastereomeric salts of ephedrine and a cyclic phosphoric acid
    Recl. Trav. Chim. Pays-Bas, 111, 111, 1992


  • Ariaans GJA, Leusen FJJ, Bruggink A
    Correlations between properties of resolving agents and the resolution process
    Chiral, 92, 1992


  • Karfunkel HR, Leusen FJJ
    Practical Aspects of Predicting Possible Crystal Structures on the Basis of Molecular Information Only
    Speedup, 6 (2), 43-50, 1992


  • Ott MA, Noordik JH
    Computer tools for reaction retrieval and synthesis planning in organic chemistry
    A brief review of their history, methods and programs, Recl. Trav. Chim. Pays-Bas 111, 239-246, 1992


  • Schaftenaar G
    MOLDEN
    QCPE-619; QCPE bulletin, 12 (3), 1992


  • van Rens GLM, van't Hullenaar R, Leunissen JAM, Bloemendal H
    Sequence analysis of the first intron of the bovine gammas-crystallin gene
    Mol. Biol. Rep, 15, 93-94, 1991 , PDF


  • Siezen RJ, de Vos WM, Leunissen JAM, Dijkstra BW
    Homology modelling and protein engineering strategy of subtilases, the family of subtilisin-like serine proteases
    Protein Engng, 4, 719-737, 1991 , PDF


  • Leunissen JAM, Noordik JH
    Sequentie analyse van eiwitten en nucleinezuur
    Computers in de chemie. 2: Toepassingen in de chemische research, JWA Klaessens (red.) SCME (SCME, Delft) vol. 26, pp. 34-45, 1991


  • Borkent JH, Ott MA, Boiten J-W
    Schermen met synthese
    Chemisch Magazine, 115-121, 1991


  • Ott MA, Noordik JH
    De computer in de organische synthese; de organische synthese in de computer
    Computers in de chemie. 2: Toepassingen in de chemische research, Klaessens, J.W.A. (Ed.), SCME (Delft, ISBN 90-72983-06-8), 62-73, 1991


  • Bloemendal M, Leunissen JAM, van Amerongen H, van Grondelle R
    Average orientation of aromatic residues in proteins determined from linear dichroism spectroscopy. A comparison of results on bovine gamma-crystallins with X-ray data
    J. Mol. Biol, 216, 181-186, 1990 , PDF


  • Leunissen JAM, ten Vergert HM, van Gelder CWG
    CAMMSA - Macro Molecular Sequence Analysis
    CAMMSA User Manual, CAOS/CAMM Center, University of Nijmegen, The Netherlands, 1990


  • Leunissen JAM, van den Hooven HW, de Jong WW
    Extreme differences in charge changes during protein evolution
    J. Mol. Evol, 31, 33-39, 1990 , PDF


  • Bruins Slot HJ, Behme HJ, Kerkkamp HEM
    Structures of the local anaesthetics ropivacaine and bupivacaine
    A structure determination and molecular-modelling study. Acta Cryst, B46, 842, 1990 , PDF


  • Blommers MJJ, Bruins Slot HJ, van der Marel BA, van Boom JH, Hilbers CW
    Conformational analysis of the 3'-5'-cyclic dinucleotide d{pApA} by means of molecular mechanics
    J. Biomol.Struct. Dyns, 8, 233, 1990 , PDF


  • Leusen FJJ, Bruins Slot HJ, Noordik JH
    Towards a rational design of resolving agents. Part III. Structural study of two pairs of diastereomeric salts of ephedrine and a cyclic phosphoric acid
    Recl. Trav. Chim, Pays-Bas 109, 523, 1990


  • van der Haest AD, Wijnberg H, Leusen FJJ, Bruggink A
    Towards a rational design of resolving agents. Part II. Correlation between resolution results and physical properties of diastereomeric salts
    Recl. Trav. Chim, Pays-Bas 109, 523, 1990


  • Leunissen J
    Eiwit- en DNA-sequentie databanken groeien steeds sneller
    Biotechnologie in Nederland, 7, 32, 1990


  • Leunissen JAM
    Sequentie databanken in de moleculaire biologie
    Chemisch Magazine, March 1990, pp. 130,133, 1990


  • Schuurmans Stekhoven FMAH, Zou YS, Swarts HGP, Leunissen J, de Pont JJHHM
    Ethylenediamine as active site probe for Na+/K+-ATPase
    Biochim. Biophys. Acta , 982, 103-114, 1989 , PDF


  • Leunissen JAM
    Computer applications in protein and nucleic acid sequence analysis
    Ph.D. Thesis, University of Nijmegen, The Netherlands, 1989


  • Leunissen JAM (interviewed by Merryn Macville)
    Onderzoek aan eiwitten werpt licht op evolutieprocessen
    Iota, Juni/Juli 1989, 8-10, 1989


  • Leunissen JAM, Borkent HJ
    De computer in de biochemie, de biochemie in de computer
    LAB/ABC , 10 (10), 30-34, 1989


  • Borkent JH, Oukes F, Noordik JH
    Chemical Reaction Searching Compared in REACCS, SYNLIB, and ORAC
    J. Chem. Inf. Comput. Sci, 28, 148-150, 1988 , PDF


  • Borkent JH
    Bereik van Molecular Modeling breidt zich uit
    Laboratorium Praktijk, 63, 1988


  • Ottenheijm HCJ, Noordik JH
    Computer Assisted Organic Synthesis (CAOS)
    Janssen Chimica Acta , 2(3), 1984