papers

Our research results by year. For a listing by category please go here.

     linked to PubMed where applicable.

2008

  1.     
    Wodak SJ, Pu S, Vlasblom J, Séraphin B.
    Challenges and rewards of interaction proteomics.
    Mol Cell Proteomics. 2008 Sep 17
  2. Malevanets A, Sirota FL, Wodak SJ.
    Mechanism and energy landscape of domain swapping in the B1 domain of protein G.
    J Mol Biol. 2008 Sep 26;382(1):223-35.
  3.     
    Pu S, Ronen K, Vlasblom J, Greenblatt J, Wodak SJ.
    Local Coherence in Genetic Interaction Patterns Reveals Prevalent Functional Versatility.
    Bioinformatics. 2008 Aug 20
  4.     
    Roca, M., De Maria, L. Wodak, S.J., Moliner, V., Tunon, I., Giraldo, J.,
    Coupling of the guanoisne glycosidic bond confirmation and the ribonucleotidecleavage reaction: Implications for barnase catalysis.
    Proteins. Feb 1.
  5.     
    Sirota FL, Héry-Huynh S, Maurer-Stroh S, Wodak SJ.
    Role of the amino acid sequence in domain swapping of the B1 domain of protein G.
    Proteins. 2008 Jan 10
  6.     
    Dessailly BH, Lensink MF, Orengo CA, Wodak SJ.
    LigASite--a database of biologically relevant binding sites in proteins with known apo-structures.
    Nucleic Acids Res. 2008 Jan
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2007

  1.     
    Wodak, S.J.,
    Docking and scoring protein complexes.
    Proteins, Structure, Function & Bioinformatics. Sept.
  2.     
    Wodak, S, J.,
    From the Mediterranean coast to the shores of Lake Ontario Capri's premiere on the American continent.
    Proteins, Structure, Function & Bioinformatics. Sept.
  3.     
    Launay, G., Mendez, R., Wodak, S. J.. & Simonson, T.
    Recognizing protein-protein interfaces with empirical potentials and reduced amino acid alphabets.
    BMC Bioinformatics 8, 270.
  4.     
    Janin, J. & Wodak, S.
    The third CAPRI assessment meeting Toronto, Canada, April 20-21, 2007.
    Structure 15, 755-9.
  5.     
    Dessailly, B.H., Lensink, M.F. & Wodak, S.J.
    Relating destabilizing regions to known functional sites in proteins.
    BMC Bioinformatics 8, 141.
  6.     
    Pu, S., Vlasblom, J., Emili, A., Greenblatt, J. & Wodak, S.J.
    Identifying functional modules in the physical interactome of Saccharomyces cerevisiae.
    Proteomics 7, 944-60.
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2006

  1.     
    Croes D, Couche F, Wodak SJ, van Helden J.
    Inferring meaningful pathways in weighted metabolic networks.
    J Mol Biol. Feb 10;356(1):222-36.
  2.     
    Krogan NJ, Cagney G, Yu H, Zhong G, Guo X, Ignatchenko A, Li J, Pu S, Datta N, Tikuisis AP, Punna T, Peregrin-Alvarez JM, Shales M, Zhang X, Davey M, Robinson MD, Paccanaro A, Bray JE, Sheung A, Beattie B, Richards DP, Canadien V, Lalev A, Mena F, Wong P, Starostine A, Canete MM, Vlasblom J, Wu S, Orsi C, Collins SR, Chandran S, Haw R, Rilstone JJ, Gandi K, Thompson NJ, Musso G, St Onge P, Ghanny S, Lam MH, Butland G, Altaf-Ul AM, Kanaya S, Shilatifard A, O'Shea E, Weissman JS, Ingles CJ, Hughes TR, Parkinson J, Gerstein M, Wodak SJ, Emili A, Greenblatt JF.
    Global landscape of protein complexes in the yeast Saccharomyces cerevisiae.
    Nature. Mar 30;440(7084):637-43. Epub Mar 22.
  3.     
    Billingsley G, Santhiya ST, Paterson AD, Ogata K, Wodak S, Hosseini SM, Manisastry SM, Vijayalakshmi P, Gopinath PM, Graw J, Heon E.
    CRYBA4, a novel human cataract gene, is also involved in microphthalmia.
    Am J Hum Genet. Oct;79(4):702-9. Epub 2006 Aug 17.
  4.     
    Vlasblom J, Wu S, Pu S, Superina M, Liu G, Orsi C, Wodak SJ.
    GenePro: a Cytoscape plug-in for advanced visualization and analysis of interaction networks.
    Bioinformatics. Sep 1;22(17):2178-9
  5.     
    Simonis N, Gonze D, Orsi C, van Helden J, Wodak SJ.
    Modularity of the transcriptional response of protein complexes in yeast.
    J Mol Biol. Oct 20;363(2):589-610
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2005

  1.     
    Croes D., Couche F., Wodak S.J., van Helden J.
    Metabolic PathFinding: inferring relevant pathways in biochemical networks.
    Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W326-30
  2.     
    Mendez R., Leplae R., Lensink M.F., Wodak S.J.
    Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures.
    Proteins. Aug 1;60(2):150-69
  3.     
    Guldener U., Munsterkotter M., Kastenmuller G., Strack N., van Helden J., Lemer C., Richelles J., Wodak S.J., Garcia-Martinez J., Perez-Ortin J.E., Michael H., Kaps A., Talla E., Dujon B., Andre B., Souciet J.L., De Montigny J., Bon E., Gaillardin C., Mewes H.W.
    CYGD: the Comprehensive Yeast Genome Database.
    Nucleic Acids Res. Jan 1;33(Database Issue):D364-8
  4.     
    Jaramillo A. and Wodak S.J.
    Protein Design is a challenge for Implicit Solvation Models.
    Biophysical J. Jan ;88(1) :156-71
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2004

  1. Wodak S.J. Castura J. and Orsi C.
    Integrative Bioinformatics: Making sense of the Networks.
    Drug Discovery Today: Technologies, 1, 1197-187
  2.     
    Mendez R. and Wodak S.J.
    Predictions of Protein-Protein Interactions: The CAPRI Experiment, Its Evaluation and Implications.
    Curr Opin Struct Biol., Apr 14(2):242-249
  3. DeMaria L. Giraldo J. and Wodak SJ.
    Shift in Equilibrium Between Folded and Extended Conformations Contributes to Increased Rate of Catalysis of GpNp versus GpN in Barnase,.
    Proteins, Structure Function and Bioinformatics Aug 1;56(2):261-276
  4.     
    Simonis N. Wodak SJ., Cohen G. and van Helden J.,
    Combining pattern discovery and discriminant analysis to predict gene co-regulation.
    Bioinformatics, April 8
  5.     
    Simonis N. van Helden J. Cohen G. and Wodak SJ.,
    Transcriptional regulation of protein complexes in Yeast.
    Genome Biology :5(5) :R33
  6.     
    Ochagavia M.E. and Wodak S.J.,
    Progressive Combinatorial algorithm for multiple structural alignments: Application to distantly related proteins.
    Proteins, Struct. Funct. And Bioinformatics. May 1 :55(2) : 436-54
  7.     
    Lemer C. Antezana E., Couche F. Fays F., Santolaria X., Janky R., Deville Y., Richelle J., and Wodak SJ.,
    The aMAZE LightBench : a Web interface to a relational database of cellular processes.
    Nucleic Acids Res., Jan 1;32 Database issue:D443-8
  8.     
    Leplae R., Hebrant A. Wodak S.J. and Toussaint A.
    ACLAME: A classification of mobile genetic elements.
    Nucleic Acids Res. 2004 Jan 1;32 Database issue:D45-9.
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2003

  1.     
    Deville Y. Gilbert D. van Helden J. and Wodak SJ.
    An overview of data models for the analysis of biochemical pathways.
    Briefing in Bioinformatics, 4, 246-259
  2.     
    Govaerts C, Bondue A, Springael JY, Olivella M, Deupi X, Le Poul E, Wodak SJ, Parmentier M, Pardo L, Blanpain C.
    Activation of CCR5 by chemokines involves an aromatic cluster between transmembrane helices 2 and 3.
    J Biol Chem. 278, 1892-903
  3.     
    Wernisch L, Wodak SJ.
    Identifying structural domains in proteins.
    Methods Biochem Anal. 44, 365-85
  4.     
    Janin J. Henrick K. Moult J., Sternberg M.J. Vajda S. Vakser I. and Wodak S.J.
    CAPRI: Critical Assessment of Predicted Interactions.
    Proteins, Structure Function and Bioinformatics, 52, 2-9
  5.     
    Mendez R. Laplae R. DeMaria L. and Wodak SJ.
    Assessment of Blind Predictions of Protein-Protein Interactions: Current Status of Docking Methods
    Proteins, Structure Function and Bioinformatics, 52, 51-67.
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2002

  1.     
    Radresa O, Ogata K, Wodak S, Ruysschaert JM, Goormaghtigh E
    Modeling the three-dimensional structure of H+-ATPase of Neurospora crassa.
    Eur J Biochem.269:5246-58
  2.     
    Ogata K, Alfonso Jaramillo, William Cohen, Jean-Paul Briand, Francine Connan, Jeannine Choppin, Sylviane Muller, and Shoshana J. Wodak
    Automatic sequence design of MHC Class-I binding peptides impairing CD8+ T cell recognition.
    J. Biol. Chem., 278 (2), 1281-1290
  3. Jaramillo A., Wernisch L., Hery S. and Wodak SJ.,
    Native protein sequences are near optimal for their structures in the protein core but not on the surface.
    Proc. Natl. Acad. Sci. USA 99(21),13554-13559
  4. Radresa, O., Ogata K., Wodak SJ., Ruysschaert JM., and Goormaghtigh E.
    Homology Modeling of the H+-ATPase of Neurospora crassa: proposal for a proton pathway from the analysis of internal polar cavities.
    Eur. J. Biochem. 269:5246-58
  5.     
    Pajon A., Vranken W., Jimenez M.A., Rico M. and Wodak S.J.
    PESCADOR: The Peptide in Solution ConformAtion Database, and Online Resource
    J. Biomolecular NMR, 23: 85-102
  6.     
    Ogata K., and Wodak S.J.
    Conserved water molecules in MHC class-I proteins and their putative structural and functions roles.
    Protein Engineering, 15:697-705
  7.     
    van Helden J. Wernisch L., Gilbert D. and Wodak S.J.
    Graph-based analysis of metabolic networks.
    Ernst Schering Res Found Workshop, 38:245-74.
  8.     
    Ochagavia M.E., Richelle J. & Wodak S.J.
    Advanced pairwise structure alignments of proteins and analysis of conformational changes.
    Bioinformatics, 18:637-640
  9.     
    Wodak S.J. & Janin J.
    The structural basis of macromolecular recognition.
    Advances in Protein Chemistry, 61: 9-73.
  10.     
    Janin J. & Wodak S.J.
    Protein modules and protein-protein interactions: towards a global view.
    Advances in Protein Chemistry 61:1-8
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2001

  1.     
    Das U, Chen S, Fuxreiter M, Vaguine AA, Richelle J, Berman HM, Wodak SJ.
    Checking nucleic acid crystal structures.
    Acta Crystallogr D Biol Crystallogr. 57:813-28.
  2.     
    Jaramillo A, Wernisch L, Hery S, Wodak SJ.
    Automatic procedures for protein design.
    Comb. Chem. High Throughput Screen. 4(8):643-59
  3.     
    Govaerts C., Lefort A., Costagliola S., Wodak S.J., Ballesteros J.A., Pardo L. & Vassart G.
    A conserved ASN in Transmembrane Helix 7 is an on/off switch in the activation of the Thyrotropin receptor
    J. Biol. Chem., 276(25), 22991-22999
  4.     
    Nadassy K.,Tomas-Oliveira I., Alberts I., Janin J. and Wodak S.J.
    Standard Atomic Volumes in Double-Stranded DNA and packing in Protein-DNA interfaces
    Nucleic Acids Res, 29(16), 3362-3376
  5.     
    Govaerts C., Blanpain C., Deupi X., Ballet S., Ballesteros, J.A., Wodak S.J., Vassart G., Pardo L. & Parmentier M.
    The TxP motif in the second transmembrane helix of CCR5: a structural determinant of chemokine-induced activation.
    J. Biol. Chem., 276 (16), 13217-13225
  6.     
    Martins J.C., Enassar M., Willem R., Wierszeski J.-M., Lippens G. & Wodak S.J.
    Solution structure of the main alpha-amylase inhibitor from amaranth seeds
    Eur. J. Biochem., 268 (8), 2379-2389.
  7. Boutonnnet N., Van Belle D. & Wodak S.J.
    Influence of ligand binding on the conformation of Torpedo californica acetylcholinesterase.
    Theor Chem Acc, 106, 10-21
  8.     
    van Helden J., Naim A., Lemer C., Mancuso R., Eldridge M., & Wodak S.J.
    From molecular activities and processes to biological function.
    Briefings in Bioinformatics, 2 (1), 81-93.
  9. Wodak S.J., Vaguine A.A., Richelle J., Das U. & Pontius J.
    Assessing the quality of Macromolecular Structures
    International Tables, Volume F Chapter 21
  10. van Helden J., Gilbert D., Wernisch L., Schroeder M. & Wodak S.
    Applications of regulatory sequence analysis and metabolic network analysis to the interpretation of gene expression data.
    Lecture Notes in Computer Sciences, 2066: 155-172.
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2000

  1.     
    van Helden J., Naim A., Mancuso R., Eldridge M., Wernisch L., Gilbert D. & Wodak S.J.
    Representing and analysing molecular and cellular function in the computer
    Biol. Chem., 381, 921-935.
  2.     
    Wernisch L., Hry S. & Wodak S.
    Automatic protein design with all atom force-fields by exact and heuristic optimization
    J. Mol. Biol., 301(3): 713-36
  3.     
    Van Belle D., De Maria L., Iurcu G. & Wodak S.J.
    Pathways of ligand clearance in acetylcholinesterase by multiple copy sampling
    J. Mol. Biol., 298(4):705-26.
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1999

  1. Oliveira I. & Wodak S.
    Thermodynamics of cavity formation in water and n-hexane using the widom particle insertion method
    J. Chem. Phys. 111(18), 8576-8587
  2. Pugliese L., Prevost M. and Wodak S.J.
    Simulations of protein unfolding: insights into the hydration.
    In Life Sciences of the Nato Science Series, Vol. 305 Hydration Processes in Biology : Theoretical and Experimental Approaches, 355-370
  3.     
    Morel N., Bon S., Greenblatt H.M., Van Belle D., Wodak S.J., Sussman J.L., Massouli J. & Silman I.
    Effect of mutations within the peripheral anionic site on the stability of acetylcholinesterase.
    Mol. Pharmacol., 55(6), 982-992
  4.     
    Wernisch L., Hunting M. & Wodak S.J.
    Identification of Structural Domains in Proteins by a Graph Heuristic.
    Proteins: Struct., Funct., Genet. 35, 338-352
  5.     
    Nadassy K., Wodak S.J. and Janin J.
    Structural features of protein-nucleic acid recognition sites .
    Biochemistry, 38 (7), 1999-2017
  6.     
    Vaguine A.V., Richelle J. & Wodak S.J.
    SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model.
    Acta Cryst. D55, 191-205
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1998

  1.     
    Giraldo J., Van Belle D. & Wodak S.J.
    Conformational Analysis of GpA and GpAp in Aqueous Solution by Molecular Dynamics and Statistical
    J. Mol. Biol., 283, 863-882.
  2.     
    Alberts I., Nadassy K. and Wodak S.J.
    Analysis of zinc binding sites in protein crystal structures
    Protein Science, 7(8), 1700-1716
  3.     
    Wintjens R., Wodak S.J. & Rooman M.
    Typical interaction patterns in alphabeta and betaalpha turn motifs.
    Protein Engineering, 11(7), 505-522
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1997

  1. Wodak S.J.
    Database derived potentials and prediction of protein structure and stability
    Encyclopedia of Computational Chemistry, P. R. Schleyer and P.R. Schreiner Editors, Wiley & Sons.
  2. EU BIOTECHNOLOGY 3D Validation project network (Wilson K.S., Butterworth S., Dauter Z., Lamzin V.S., Wodak S.J., Pontius J., Richelle J., Vaguine A., Sander C., Hooft R.W.W., Vriend G., Thornton J.M., Laskowski R.A., MacArthur M.W., Dodson E.J., Murshudov G., Oldfield T.J., Kaptein R., Rullmann J.A.C.
    (1997). Who checks the checkers? Four validation tools applied to eight atomic resolution structures.
    J. Mol. Biol. 276, 417-436
  3. Wodak S.J., Pontius J., Vaguine A. and Richelle J.
    Procedures for assessing the quality of X-ray structures of macromolecules
    In Proceedings of the 1996 meeting of the IUCr Macromolecular Computing School.
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1996

  1.     
    Kocher J.-P.A., Prvost M., Wodak S.J. & Lee B.K.
    Properties of the protein matrix revealed by the free energy of cavity formation.
    Structure, 4(12), 1517-1529
  2.     
    Pontius J., Richelle J. and Wodak S.J.
    Deviations from standard atomic volumes as a quality measure for protein crystal structures.
    J. Mol. Biol., 264(1), 121-136
  3.     
    EU BRIDGE Database project consortium: Gray P.M.D., Kemp G.J.L., Rawlings C.J., Brown N.P., Sander C., Thornton J.M., Orengo C.M., Wodak S.J. & Richelle J.
    Molecular structure information and databases.
    TIBS, 21(7), 251-256
  4.     
    Wodak S.J.
    Extending molecular systematics to the third dimension.
    Nature Structural Biology, 3(7), 575-578.
  5.     
    Gordon-Beresford R.M.H., Van Belle D., Giraldo J. & Wodak S.J.
    Effect of nucleotide substrate binding on the pKa of catalytic residues in barnase Proteins:
    Struct., Funct., Genet. 25, 180-194
  6. Horvath D., Van Belle D., Lippens G. and Wodak S.J.
    Development and parametrization of continuum solvent models. I-Models based on the boundaryelement method.
    J. Chem Phys. 104(7), 6679-6695
  7. Prvost M., Oliveira I.T., Kocher J.-P. & Wodak S.J.
    Free energy of cavity formation in liquid water and hexane
    J. Phys. Chem. 100(7), 2738-2743.
  8.     
    Wintjens R.T., Rooman M.R. and Wodak S.J.
    Automatic classification and analysis of aa-turn motifs in proteins.
    J. Mol. Biol. 255(1), 235-253
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1995

  1. Wodak S.J., Rooman M.J. and Kocher J.-P.A.
    Effective potentials derived from known protein structures and their use in predicting 3D structure from sequence.
    In F. Sanz, J. Giraldo and F. Manaut (eds.) QSAR and Molecular Modelling: Concepts, computational tools and biological applications. Proceedings of the 10th European Symposium on Structure-Activity Relationships: QSAR and Molecular Modelling, Barcelona, Spain, September 4-5, 1994. J.R. Prous Science Publishers, Barcelona (Spain), 206-215.
  2.     
    Lemer C.M.-R., Rooman M.J. and Wodak S.J.
    Protein structure prediction by threading methods: evaluation of current techniques.
    Proteins: Struct., Funct., Genet. 23(3), 337-355
  3.     
    Boutonnet N.S., Rooman M.J. and Wodak S.J.
    Automatic analysis of protein conformational changes by multiple linkage clustering.
    J. Mol. Biol. 253(4), 633-647
  4.     
    Rooman M.J. and Wodak S.J.
    Are database-derived potentials valid for scoring both forward and inverted protein folding?
    Protein Engineering 8(9), 849-858
  5.     
    Kajava A., Vassart G. and Wodak S.J.
    Modeling of the three-dimensional structure of proteins with the most typical leucine-rich repeats.
    Structure 3(9), 867-877
  6. Van Belle D. and Wodak S.J.
    Extended Lagrangian formalism applied to temperature control and electronic polarization effects in molecular dynamics simulations
    Computer Physics Communications 91, 253-262
  7.     
    Boutonnet N.S., Rooman M.J., Ochagavia M.-E., Richelle J. and Wodak S.J.
    Optimal protein structure alignments by multiple linkage clustering: application to distantly related proteins.
    Protein Eng. 8(7), 647-662
  8.     
    Pugliese L., Prvost M. and Wodak S.J.
    Unfolding simulations of the 85-102 b-hairpin of barnase
    J. Mol. Biol. 251(3), 432-447
  9. Wodak S.J., Van Belle D. and Prvost M.
    Molecular dynamics and free energy calculations applied to the enzyme barnase and one of its stability mutants.
    In J. Goodfellow (ed.) Computer modelling in molecular biology, VCH, Weinheim, 61-102
  10. Wodak S.J., Pontius J.U.,Vaguine A. and Richelle J.
    Validating protein structures: from consistency checking to quality assessment
    In W.N. Hunter, J.M. Thornton and S. Bailey (eds.) Making the Most of your Model. Proceedings of the CCP4 study weekend held at Chester, United Kingdom, 1995, 41-51.
  11.     
    Lippens G., Najib J., Wodak S.J. and Tartar A.
    NMR sequential assignments and solution structure of chlorotoxin, a small scorpion toxin that blocks chloride channels.
    Biochemistry 34(1), 13-21
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1994

  1. Rooman M.J., Kocher J.-P.A., Wintjens R. and Wodak S.J.
    Knowledge based potentials for predicting the three-dimensional conformation of proteins.
    In S. Doniach (ed.) Statistical mechanics, protein structure, and protein substrate interactions. Plenum Press, New York. Proceedings of a NATO meeting held at Cargse, France, 1993, 327-330
  2. Wodak S.J. and Prvost M.
    Origins of mutation induced stability changes in barnase: an analysis based on free energy calculations.
    In S. Doniach (ed.) Statistical mechanics, protein structure, and protein substrate interactions. Plenum Press, New York. Proceedings of a NATO meeting held at Cargse, France, 1993, 63-74.
  3. Van Belle D., Prvost M., Lippens G. and Wodak S.J.
    Influence of induced water dipoles on computed properties of liquid water and on hydration and association of non-polar solutes
    In C.J. Cramer and D.G. Truhlar (eds.) ACS Symposium Series volume 568 Structure and Reactivity in Aqueous Solution: Characterization of chemical and biological systems. 207th National Meeting of the American Chemical Society, San Diego, Ca., March 1994, 318-334
  4. Wintjens R.T., Rooman M.J. and Wodak S.J.
    Identification of short turn motifs in proteins using sequence and structure fingerprints Isr. J.
    Chem. 34 (2), 257-269
  5.     
    Pintar A., Chollet A., Bradshaw C., Chaffotte A., Cadieux C., Rooman M.J., Hallenga K., Knowles, Goldberg M. and Wodak S.J.
    Conformational properties of four peptides corresponding to a-helical regions of Rhodospirillum cytochrome c2 and bovine calcium binding protein.
    Biochemistry 33 (37), 11158-11173
  6.     
    Cerf C., Lippens G., Ramakrishnan V., Muyldermans S., Segers A., Wyns L., Wodak S.J. and Hallenga K.
    Homo- and heteronuclear 2D NMR studies of the globular domain of histone H1: full assignment, tertiary structure, and comparison with the globular domain of histone H5
    Biochemistry 33 (37), 11079-11086
  7.     
    Gutschina A., Sansom Cl., Prvost M., Richelle J., Wodak S.J., Wlodawer Al. and Weber I.T.
    Energy calculations and analysis of HIV-1 protease-inhibitor crystal structures.
    Protein Eng. 7(3), 309-317
  8.     
    Kocher J.-P., A., Rooman M.J. and Wodak S.J.
    Factors influencing the ability of knowledge based potentials to identify native sequence-structure matches
    J. Mol. Biol. 235(5), 1598-1613
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1993

  1. Lippens G., Van Belle D., Wodak S.J. and Jeener J.
    T1 relaxation time of water from a molecular dynamics simulation.
    Mol. Phys. 80(6), 1469-1484
  2.     
    Cerf C., Lippens G., Muyldermans S., Segers A., Ramakrishnan V., Wodak S.J., Hallenga K. and Wyns L.
    Homo- and heteronuclear 2D NMR studies of the globular domain of histone H1: sequential assignment and secondary structure.
    Biochemistry 32(42), 11345-11351
  3.     
    Lippens G., Hallenga K., Van Belle D., Wodak S.J., Nirmala N.R., Hill P., Russell K.C., Smith D.D. and Hruby V.J.
    Transfer NOE study of the conformation of oxytocin bound to bovine neurophysin I
    Biochemistry 32(36), 9423-9434.
  4. Wodak S.J. and Rooman M.J.
    Generating and testing protein folds.
    Curr. Opin. Struct. Biol. 3, 247-259.
  5. Prvost M., Wodak S.J., Tidor B. and Karplus M.
    Analysis of the stability of mutants Ile96 into Val and into Ala in barnase, based on free energy mutations.
    In Cahiers IMABIO (eds. CNRS) Prdiction structurale et dynamique molculaire des protines, 7, 45-48
  6. Wodak S.J., Van Belle D. and Prvost M.
    Molecular dynamics simulations of a protein-water system: analysis of structural and electrostatic properties.
    In Cahiers IMABIO (eds. CNRS) Prdiction structurale et dynamique molculaire des protines, 7, 39-43
  7. Pintar A., Chollet A., Rooman M.J., Cerf C. and Wodak S.J.
    1H-NMR studies of protein fragments in solution.
    Journal of Cellular Biochemistry (XXII Annual Keystone Symposia on Molecular & Cellular Biology Frontiers of NMR in Molecular Biology III), suppl. 17C, 282
  8. Rooman, M.J., Wodak, S.J., and Kocher, J.-P.
    Prediction of regions with well defined conformational preferences in proteins, and their relevance to protein folding.
    In M. Doyama, J. Kihara, M. Tanaka and R. Yamamoto (eds.) Computer Aided Innovation of New Materials II. Elsevier Science Publishers b.v., 1129-1235.
  9. Van Belle D. and Wodak S.J.
    Molecular dynamics study of methane hydration and methane association in a polarizable water phase.
    J. Am. Chem. Soc., 115(2), 647-652
  10.     
    Janin J. and Wodak, S.J.
    The quaternary structure of Carbonmonoxy Hemoglobin Ypsilanti.
    Proteins, 15, 1-4
  11. Wodak S.J., Van Belle D. and Prvost M.
    Molecular dynamics simulations and free energy calculations of barnase and two stability mutants.
    In Proceedings of INSERM workshop 49 Molecular modelling and graphics applied to structure-function relationships (Le Vsinet, France, November 1992)
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1992

  1.     
    Rooman M.J. and Wodak S.J.
    (1992)Extracting information on folding from the amino acid sequence: role of consensus stable regions in homologous proteins
    Biochemistry, 31, 10239-10249
  2.     
    Rooman M.J., Kocher J.-P., and Wodak S.J.
    Extracting information on folding from the amino acid sequence: accurate predictions for protein regions with stable conformation in absence of tertiary interactions
    Biochemistry, 31, 10226-10238
  3. Van Belle D., Froeyen, M., and Wodak S.
    Molecular dynamics simulation of polarizable water by the extended Langrangian method.
    Molecular Physics, 77(2), 239-255
  4.     
    van Tilbeurgh H., Jenkins J., Chiadmi M., Janin J., Wodak S.J., Mrabet, N.T., and Lambeir A.-M.
    Protein engineering of xylose (glucose) isomerase from Actinoplanes missouriensis 3. Changing metal specificity and the pH profile by site-directed mutagenesis.
    Biochemistry, 31(24), 5467-5471
  5.     
    Lambeir A.-M., Lauwereys M., Stanssens P., Mrabet N.T., Snauwaert J., van Tilbeurgh H., Matthyssens G., Lasters I., De Maeyer M., Wodak S.J., Jenkins J., Chiadmi M. and Janin J.
    Protein engineering of xylose (glucose) isomerase from Actinoplanes missouriensis 2. Site-directed mutagenesis of the xylose binding site.
    Biochemistry, 31(24), 5459-5466.
  6.     
    Jenkins J., Janin J., Rey, F., Chiadmi M., van Tilbeurgh H., Lasters I., De Maeyer M., Van Belle D., Wodak S.J., Lauwereys M., Stanssens P., Mrabet N.T., Snauwaert J., Matthyssens G. and Lambeir A.-M.
    Protein engineering of xylose (glucose) isomerase from Actinoplanes missouriensis 1. Crystallography and site-directed analysis of metal binding sites.
    Biochemistry, 31(24), 5449-5458
  7.     
    Scheerlinck J.-P. Y., Lasters I., Claessens M., De Maeyer M., Pio F., Delhaise Ph., Wodak S.
    Recurrent alpha beta loop structures in TIM barrel motifs show a distinct pattern of conserved structural features.
    Proteins, 12(4), 299-313
  8. Mrabet N.T., Van den Broeck A., Van den Brande I., Stanssens P., Laroche Y., Lambeir A.-M., Matthyssens G., Jenkins J., Chiadmi M., van Tilbeurgh H., Rey F., Janin J., Quax W., Lasters I., De Maeyer M. and Wodak S.J.
    Arginine residues as stabilizing elements in proteins.
    Biochemistry 31(8), 2239-2253
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1991

  1.     
    Karplus M., Prvost M., Tidor B. and Wodak S.
    Simulation analysis of the stability mutants R96H of T4 lysozyme and I96A in barnases in Protein Conformation,
    CIBA. Foundation Symposium 161, Wiley-Chichester, 63-74.
  2. Gordon-Beresford R.M.H., Coulombeau C., and Wodak S.J.
    Modelling enzyme-oligonucleotide interactions in barnase.
    J.Chim.Phys. 88, 2653-2658.
  3. Janin J., Rey F., Jenkins J., Chiadmi M., van Tilbeurgh H., Mrabet N., van der Broeck A., van den Brande I., Stanssens P., Laroche Y., Lambeir A.-M., Lauwereys M., Matthyssens G., Lasters I., de Maeyer M., and Wodak S.
    Ingnierie d'un enzyme industriel : la glucose isomrase de Actinoplanes missouriensis
    In Ecole Polytechnique, Palaiseau (eds.), Conception, slection, production et analyse des protines de nouvelle gnration, XIV colloquium organized by la section de microbiologie industrielle et de biotechnologie of the Socit franaise de microbiologie, 125-136.
  4.     
    Prvost M., Wodak S.J., Tidor B. and Karplus M.
    Contribution of the hydrophobic effect to protein stability; analysis based on simulations of the Ile-96 -> Ala mutation in barnase.
    Proc.Natl.Acad.Sci.USA 88(23), 10880-10884.
  5. Wodak S.J., Prvost M., Tidor B, and Karplus M.
    Analysis of the stability mutant ILE96!ALA in barnase, based on free energy simulations
    In R. Lavery, J.-L. Rivail & J. Smith (eds.) Advances in Biomolecular Simulations, Joint International Conference of IBM and Division de Chimie Physique (SFC), Obernai, France 1991, American Institute of Physics Conference Proceedings, 239, 283-292.
  6.     
    Rooman M.J., Kocher J.-P.A. and Wodak S.J.
    Prediction of protein backbone conformation based on 7 structure assignments: Influence of local interactions.
    J.Mol.Biol. 221, 961-979.
  7. Alard Ph. and Wodak S.J.
    Detection of cavities in a set of interpenetrating spheres.
    Journal of Computational Chemistry 12(8), 918-922.
  8.     
    Huysmans M., Richelle J. and Wodak S.J.
    SESAM: a relational database for structures of macromolecules.
    Proteins 11 (1), 59-76.
  9. Mrabet N., Lambeir A.-M., Jenkins J., Chiadmi M., van Tilbeurgh H., Janin J., Quax W., Lasters I., De Maeyer M., Stanssens P., Matthyssens G., and Wodak S.J.
    Arginine residues as stabilizing elements in proteins.
    In J. Balan (ed.) Metabolism and enzymology of nucleic acids including gene and protein engineering (Proceedings of the VIIth International Symposium on Metabolism and Enzymology of Nucleic Acids including Gene and Protein Engineering), 7, 63-67.
  10.     
    Rooman M.J. and Wodak S.J.
    Weak correlation between predictive power of individual sequence patterns and overall prediction accuracy in proteins.
    Proteins 9 (1), 69-78.
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1990

  1.     
    Wodak S.J., Lasters I., Pio F. and Claessens M.
    Basic design features of the parallel ab barrel, a ubiquitous protein folding motif.
    In J. Kay, G.G. Lunt and D.J. Osguthorpe (eds.) Protein Structure, Prediction and Design, Biochem. Soc. Symp., 57, 99-121.
  2. Moens L., Wolf G., Van Hauwaert M.L., De Baere I., Van Beumen J., Wodak S.J., and Trotman C.N.A.
    The extracellular hemoglobins of Artemia: Structure of the oxygen carrier and respiration physiology.
    In Artemia Biology, CRC Press (Browne, Sorgeloos and Trotman Editors), 187-220.
  3. Prvost M., Van Belle D., Lippens G. and Wodak S.
    Computer simulations of liquid water: Treatment of long-range interactions.
    Molecular Physics 71 (3), 587-603.
  4.     
    Moens L., Van Hauwaert M.-L., De Smet K., Ver Donck K., Van de Peer, Y., Van Beumen J., Wodak S.J., Alard Ph. and Trotman C.
    Structural interpretation of the amino acid sequence of a second domain from the Artemia covalent polymer globin.
    J.Biol.Chem. 265 (24), 14285-14291.
  5. Wodak S.J., Van Belle D., Froeyen M. and Prvost M.
    Molecular dynamics simulations of a solvated protein: analysis of structural and electrostatic properties.
    In Rivail (ed.) Modeling of Molecular Structures and Properties (Proceedings of an International Meeting, Nancy, France, 11-15 September 1989). Studies in Physical and Theoretical Chemistry, 71, 491-513.
  6.     
    Lasters I., Wodak, S.J. and Pio, F.
    The design of idealized a/b-barrels: analysis of b-sheet closure requirements.
    Proteins 7, 249-256.
  7.     
    Rooman M.J., Rodriguez J. and Wodak S.J.
    Relations between protein sequence and structure and their significance.
    J.Mol.Biol. 213, 337-350.
  8.     
    Rooman M.J., Rodriguez J. and Wodak S.J.
    Automatic definition of recurrent local structure motifs in proteins.
    J.Mol.Biol. 213, 327-336.
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1989

  1.     
    Rooman M., Wodak S.J. and Thornton J.
    Amino acid sequence templates derived from recurrent turn motifs in proteins: critical evaluation of their predictive power.
    Protein Engineering 3, 23-27.
  2. Van Belle D., Prvost M. and Wodak S.J.
    Electrostatic properties of solvated proteins: a microscopic analysis based on computer simulations.
    Proceedings of the Nobel Symposia Chemical Scripta 29A, 181-189.
  3. Wodak S.J. and Van Montagu M.
    Industrial and Agricultural Applications.
    Special issue of Biotech, March 1989, 72-76.
  4.     
    Claessens M., Van Cutsem E., Lasters I. and Wodak S.J.
    Modelling the polypeptide backbone with 'spare parts' from known protein structures.
    Protein Engineering 2, 335-345.
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1988

  1.     
    Rey F., Jenkins J., Janin J., Lasters I., Alard P., Claessens M., Matthyssens G. and Wodak S.J.
    Structural analysis of the 2.8 model of xylose isomerase from Actinoplanes missouriensis.
    Proteins 4, 165-172.
  2.     
    Rooman M.J. and Wodak S.J.
    Identification of predictive sequence motifs limited by protein structure database size.
    Nature 335, 45-49
  3.     
    Moens L., Van Hauwaert M.-L., De Smet K., Geelen D., Verpooten G., Van Beeumen J., Wodak S.J., Alard Ph. and Trotman C.
    (1988). A structural domain of the covalent polymer globin chains of Artemia - Interpretation of amino acids sequence data.
    J.Biol.Chem. 263, 4679-4685
  4. Wodak S.J. and Van Montagu M.
    State of the art in protein engineering and its application to enzymes and proteins in industry and agriculture.
    In Interbiotech '87, Enzyme Technologies, A. Blazej and J. Zemek (eds.), Proceedings of the International symposium on Biotechnology, Bratislava, Czechoslovakia, June 25-26, 1987, Elsevier, Amsterdam, 69-78.
  5.     
    Lasters I., Wodak S.J., Alard P. and Van Cutsem E.
    Structural principles of parallel beta-barrels in proteins.
    Proc.Natl.Acad.Sci.USA 85, 3338-3342.
  6. Claessens M., Alard P., Lasters I and Wodak S.J.
    Fragment-matching approach to protein backbone building: a tool for structural analysis.
    In ICSU short report, vol.8, pp 13.
  7. Wodak S.J.
    Computer Graphics as an Aid in Protein Structure-Function Analysis and Design In Macromolecular Biorecognition, Irwin Chaiken, Emilia Chiancone, Angelo Fontana and Paolo Neri (eds.),.
    The Humana Press, Inc., 3-11
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1987

  1. Van Cutsem E. and Wodak S.J.
    Prediction of the tertiary structure of proteins from homologous proteins of known structure. Application: prediction of the triose phosphate isomerase of Trypanosoma brucei.
    Archives Internationales de Physiologie et de Biochimie 95 (3), B149.
  2. Wodak S.J.
    La simulation par ordinateur.
    Biofutur 62, 39-42.
  3.     
    Wodak S.J., De Crombrugghe M. and Janin J.
    Computer studies of interactions between macromolecules.
    Prog.Biophys.Mol.Biol. 49, 29-63.
  4. Wodak S.J.
    Computer aided design and Protein Engineering.
    Annals of the New York Academy of Sciences 501, 1-13.
  5.     
    Van Belle D., Couplet I., Prvost M. and Wodak S.J.
    Calculations of electrostatic properties in proteins. Analysis of contributions from induced protein dipoles.
    J.Mol.Biol. 198, 721-735.
  6. Van Cutsem E., T.T.Teeri, Lehtovaara P., Knowles J. and Wodak S.J.
    Molecular modelling of the proposed active site region of the Trichoderma Reesei Cellobiohydrolase.
    I. Protein Engineering 87, pp 38.
  7. Wodak S.J., Couplet I., Van Belle D. and Prvost M.
    Electrostatic interactions in proteins: towards more detailed microscopic representations.
    J. of Cellular Biochemistry supplement 11C, pp. 221.
  8. Lasters I., Wodak S.J. and Alard P.
    Geometrical principles governing b-strand parity in 8 stranded b-barrel proteins.
    J. of Cellular Biochemistry supplement 11C, pp. 226
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1986

  1. Wodak S.J.,
    Protein Design by computers.
    Chemisch Magazine 18, 381-384
  2. Wodak S.J.,
    Mutations by computer.
    Chemisch Magazine 18, 324-325.
  3. Wodak S.J.,
    Mechanisms of conformational changes in Proteins.
    In Computer Aided Molecular Design, IBC, Technical Services Ltd Publications.
  4. Barnes W.M., Blckner H., Krawinkel U., Lehrach H., Marquardt R., Smith M., Van Montagu M., Weglenski P., Winter G. and Wodak S.J.
    Silver, S. (ed.) Biotechnology: Potentials and Limitations. Dahlem Konferenzen. Berlin, Heidelberg, New York, Tokyo
    Springer-Verlag, pp 5 -18.
  5.     
    Wodak S.J., Decoen J.-L., Edelstein S.J., Demarne H. and Beuzard Y.
    Modification of human hemoglobin by Glutatione - III.Perturbations of hemoglobin conformation analysed by computer modelling.
    J.Biol.Chem. 261, 14717-14724.
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1985

  1. Wodak, S.J. and De Meyts, P.
    Molecular Graphics in Europe: an appraisal of current capabilities, future needs and possibilities
    Published by the EEC for limited circulation.
  2. Wodak, S.J., Delhaise, Ph., Bardiaux, M., Alard, Ph., Van Belle, D. and Marchal, B.
    Towards computer aided protein design.
    J. of Cellular Biochemistry supplement 9B pp 140.
  3. Marchal, B., Kennes, R., Bardiaux, M. and Wodak, S.,
    A semantical approach to protein structure prediction.
    Journal of Molecular Graphics 3, 113-114.
  4.     
    Lesk, A.M., Janin, J., Wodak, S.J. and Chothia, C.
    Haemoglobin: the surface buried between the alpha 1 beta 1 and alpha 2 beta 2 dimers in the deoxy and oxy structures.
    J.Mol.Biol. 183, 267-270.
  5. Delhaise, P., Van Belle, D., Bardiaux, M., Alard, P., Hamers, P., Van Cutsem, E. a and Wodak, S.J.
    Analysis of data from computer simulations on macromolecules using the CERAM package.
    Journal of Molecular Graphics 3, 116-119
  6.     
    Wodak, S.J., Alard, Ph., Delhaise, Ph., and Renneboog-Squilbin, C.
    Simulation of conformational changes in 2 Zn Insulin.
    J.Mol.Biol. 181, 317-322.
  7. Janin, J. and Wodak, S.J.
    Reaction pathway for the quaternary structure change in haemoglobin.
    Biopolymers 24, 509-526
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1984

  1. Wodak, S.J.
    Graphique molculaire et conception assiste par ordinateur de protines
    Technologie Transfert Express 9, 6-10
  2. Wodak, S.J.
    Graphique molculaire et conception de protines assiste par ordinateur
    Compte-rendu du colloque CFAO l'Universit Libre de Bruxelles.
  3. Delhaise, Ph., Bardiaux, M. and Wodak, S.J.
    Interactive computer animation of macromolecules.
    Journal of Molecular Graphics 2, 103-106Journal of Molecular Graphics 2, 103-106
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1983

  1.     
    Janin, J. and Wodak, S.J.
    Structural domains in proteins and their role in the dynamics of protein function.
    Progr.Biophys.Molec.Biol. 42, 21-78.
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1982

  1. Michel, A., Durant, F. and Wodak, S.J.
    Etude conformationnelle des complexes de l'alpha-chymotrypsine.
    Eur.J.Med.Chem.-Chim.Ther. 17, 6, 521-525.
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1981

  1. Renneboog, C., Delhaise, Ph. and Wodak, S.J.
    The influence of crystal packing on the 3-D conformation of insulin.
    Archives Internationales de Physiologie et de Biochimie 89, B192.
  2. Delhaise, Ph. and Wodak, S.J.
    3-D conformation of insulin in the 2 zinc crystal: an analysis based on the minimization of empirical energy functions.
    In Report of the CECAM Workshop on Non-bonded interactions and the specificity of protein association and folding, Brussels, 122-160.
  3. Wodak, S.J. and Janin, J.
    Preliminary analysis of the reaction pathway for the quaternary transition in hemoglobin using energy refinement and molecular graphics.
    In Report of the CECAM Workshop on Non-bonded interactions and the specificity of protein association and folding, Brussels, 47-64
  4. Janin, J. and Wodak, S.J.
    A docking algorithm applied to protein-protein association and to the allosteric mechanism of haemoglobin.
    In Report of the CECAM Workshop on Non-bonded interactions and the specificity of protein association and folding, Brussels, 5-46.
  5.     
    Wodak, S.J., and Janin, J.
    Location of structural domains in proteins.
    Biochemistry 20, 6544-6552
  6. Wodak, S.J.
    Is it possible to deduce the interaction between two proteins from their 3-D structure?
    In Molecular basis of mutant hemoglobin dysfunction, P. Siegler (Ed.).Amsterdam, Elsevier/North Holland, 199-211.
  7. Delhaise, Ph., and Wodak, S.J.
    Prograph: an interactive graphic system dedicated to the visualisation and manipulation of biological macromolecules.
    In Structural aspects of recognition and assembly in biological macromolecules, Vol. 1, Balaban (Ed.). Revohot, International Sciences Services, 169-181.
  8. Wodak, S.J. and Janin, J.
    Defining compact domains in globular proteins. In Structural aspects of recognition and assembly in biological macromolecules,
    Vol 1, Balaban (Ed.). Revohot, International Sciences Services, 149-167.
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1980

  1.     
    Wodak, S.J. and Janin, J.
    Analytical approximation to the accessible surface area of proteins.
    Proc.Natl.Acad.Sci.USA 77, 1736-1740.
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1979

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1978

  1.     
    Wodak, S.J. and Janin, J.
    A computer analysis of protein-protein interaction.
    Arch.Int.Physiol.Biochim. 86, 473-474
  2.     
    Janin, J., Wodak, S.J., Levitt, M. and Maygret, B.
    Conformation of amino acid side-chains in proteins.
    J.Mol.Biol. 125, 357-386.
  3.     
    Wodak, S.J. and Janin, J.
    Computer analysis of protein-protein interaction.
    J.Mol.Biol. 124, 323-342
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1977

  1. Wyckoff, H.W., Carlson, W. and Wodak S.J.
    The structure of nucleic-acid protein complexes as evidenced by dinucleoside complexes with RNase-S. In Nucleic acid-protein recognition.
    New York, Academic Press., 569-580.
  2.     
    Wodak, S.J., Liu, M.Y. and Wyckoff, H.W.
    The structure of cytidilyl-(2',5')-adenosine, when bound to pancreatic ribonuclease. S J.Mol.Biol. 116, 855-875.
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1976

  1.     
    Chothia, C., Wodak, S.J. and Janin, J.
    Role of subunit interfaces in the allosteric mechanism of haemoglobin.
    Proc.Natl.Acad.Sci.U.S.A. 73, 3793-3797.
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1975

  1. Wodak, S.J., Kahn, P., Dadivinian, A.K. and Levinthal, C. (1975)
    Hemoglobin interaction in sickle cell fibers: theoretical approaches to the molecular contacts. In Environmental effects on molecular structure and properties,
    B. Pullman (Ed), Dordrecht, D. Reidel Publishing Company, 389-407.
  2.     
    Levinthal, C., Wodak, S.J., Kahn, P. and Dadivanian, A.K. (1975)
    Hemoglobin interaction in sickle cell fibers. I: Theoretical approaches to the molecular contacts.
    Proc.Natl.Acad.Sci.U.S.A. 72, 1330-1334.
  3. Wodak, S.J.
    The crystal structure of Heliotrine, a pyrrolizidine alkaloid monester Acta Cryst. 31, 569-573.
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1974

  1. Levinthal, C., Kahn, P., Wodak, S.J. and Dadivanian, A.
    Molecular contacts in Hb-S fiber formation. In Proceedings of the first national symposium on sickle cell disease, Washington D.C., U.S.A.
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1973

  1. Sussman, J.L. and Wodak, S.J.
    The crystal structure of Fulvine, a pyrrolizidine alkaloid Acta Cryst. 29, 2918-2926.
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