Papers - Wodak Lab

2008

• PubMed
  Wodak SJ, Pu S, Vlasblom J, Séraphin B.
  Challenges and rewards of interaction proteomics.
  Mol Cell Proteomics. 2008 Sep 17
• 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.
• PubMed
  Pu S, Ronen K, Vlasblom J, Greenblatt J, Wodak SJ.
  Local Coherence in Genetic Interaction Patterns Reveals Prevalent Functional Versatility.
  Bioinformatics. 2008 Aug 20
• PubMed
  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.
• PubMed
  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
• PubMed
  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

2007

• PubMed
  Wodak, S.J.,
  Docking and scoring protein complexes.
  Proteins, Structure, Function & Bioinformatics. Sept.
• PubMed
  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.
• PubMed
  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.
• PubMed
  Janin, J. & Wodak, S.
  The third CAPRI assessment meeting Toronto, Canada, April 20-21, 2007.
  Structure 15, 755-9.
• PubMed
  Dessailly, B.H., Lensink, M.F. & Wodak, S.J.
  Relating destabilizing regions to known functional sites in proteins.
  BMC Bioinformatics 8, 141.
• PubMed
  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.

2006

• PubMed
  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.
• PubMed
  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.
• PubMed
  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.
• PubMed
  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
• PubMed
  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

2005

• PubMed
  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
• PubMed
  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
• PubMed
  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
• PubMed
  Jaramillo A. and Wodak S.J.
  Protein Design is a challenge for Implicit Solvation Models.
  Biophysical J. Jan ;88(1) :156-71

2004

• Wodak S.J. Castura J. and Orsi C.
  Integrative Bioinformatics: Making sense of the Networks.
  Drug Discovery Today: Technologies, 1, 1197-187
• PubMed
  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
• 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
• PubMed
  Simonis N. Wodak SJ., Cohen G. and van Helden J.,
  Combining pattern discovery and discriminant analysis to predict gene co-regulation.
  Bioinformatics, April 8
• PubMed
  Simonis N. van Helden J. Cohen G. and Wodak SJ.,
  Transcriptional regulation of protein complexes in Yeast.
  Genome Biology :5(5) :R33
• PubMed
  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
• PubMed
  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
• PubMed
  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.

2003

• PubMed
  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
• PubMed
  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
• PubMed
  Wernisch L, Wodak SJ.
  Identifying structural domains in proteins.
  Methods Biochem Anal. 44, 365-85
• PubMed
  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
• PubMed
  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.

2002

• PubMed
  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
• PubMed
  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
• 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
• 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
• PubMed
  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
• PubMed
  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
• PubMed
  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.
• PubMed
  Ochagavia M.E., Richelle J. & Wodak S.J.
  Advanced pairwise structure alignments of proteins and analysis of conformational changes.
  Bioinformatics, 18:637-640
• PubMed
  Wodak S.J. & Janin J.
  The structural basis of macromolecular recognition.
  Advances in Protein Chemistry, 61: 9-73.
• PubMed
  Janin J. & Wodak S.J.
  Protein modules and protein-protein interactions: towards a global view.
  Advances in Protein Chemistry 61:1-8

2001

• PubMed
  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.
• PubMed
  Jaramillo A, Wernisch L, Hery S, Wodak SJ.
  Automatic procedures for protein design.
  Comb. Chem. High Throughput Screen. 4(8):643-59
• PubMed
  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
• PubMed
  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
• PubMed
  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
• PubMed
  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.
• 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
• PubMed
  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.
• Wodak S.J., Vaguine A.A., Richelle J., Das U. & Pontius J.
  Assessing the quality of Macromolecular Structures
  International Tables, Volume F Chapter 21
• 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.

2000

• PubMed
  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.
• PubMed
  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
• PubMed
  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.

1999

• 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
• 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
• PubMed
  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
• PubMed
  Wernisch L., Hunting M. & Wodak S.J.
  Identification of Structural Domains in Proteins by a Graph Heuristic.
  Proteins: Struct., Funct., Genet. 35, 338-352
• PubMed
  Nadassy K., Wodak S.J. and Janin J.
  Structural features of protein-nucleic acid recognition sites .
  Biochemistry, 38 (7), 1999-2017
• PubMed
  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

1998

• PubMed
  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.
• PubMed
  Alberts I., Nadassy K. and Wodak S.J.
  Analysis of zinc binding sites in protein crystal structures
  Protein Science, 7(8), 1700-1716
• PubMed
  Wintjens R., Wodak S.J. & Rooman M.
  Typical interaction patterns in alphabeta and betaalpha turn motifs.
  Protein Engineering, 11(7), 505-522

1997

• 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.
• 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
• 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.

1996

• PubMed
  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
• PubMed
  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
• PubMed
  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
• PubMed
  Wodak S.J.
  Extending molecular systematics to the third dimension.
  Nature Structural Biology, 3(7), 575-578.
• PubMed
  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
• 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
• 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.
• PubMed
  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

1995

• 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.
• PubMed
  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
• PubMed
  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
• PubMed
  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
• PubMed
  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
• 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
• PubMed
  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
• PubMed
  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
• 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
• 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.
• PubMed
  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

1994

• 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
• 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.
• 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
• 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
• PubMed
  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
• PubMed
  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
• PubMed
  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
• PubMed
  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

1993

• 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
• PubMed
  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
• PubMed
  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.
• Wodak S.J. and Rooman M.J.
  Generating and testing protein folds.
  Curr. Opin. Struct. Biol. 3, 247-259.
• 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
• 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
• 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
• 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.
• 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
• PubMed
  Janin J. and Wodak, S.J.
  The quaternary structure of Carbonmonoxy Hemoglobin Ypsilanti.
  Proteins, 15, 1-4
• 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)

1992

• PubMed
  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
• PubMed
  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
• 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
• PubMed
  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
• PubMed
  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.
• PubMed
  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
• PubMed
  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
• 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

1991

• PubMed
  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.
• Gordon-Beresford R.M.H., Coulombeau C., and Wodak S.J.
  Modelling enzyme-oligonucleotide interactions in barnase.
  J.Chim.Phys. 88, 2653-2658.
• 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.
• PubMed
  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.
• 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.
• PubMed
  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.
• Alard Ph. and Wodak S.J.
  Detection of cavities in a set of interpenetrating spheres.
  Journal of Computational Chemistry 12(8), 918-922.
• PubMed
  Huysmans M., Richelle J. and Wodak S.J.
  SESAM: a relational database for structures of macromolecules.
  Proteins 11 (1), 59-76.
• 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.
• PubMed
  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.

1990

• PubMed
  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.
• 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.
• 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.
• PubMed
  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.
• 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.
• PubMed
  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.
• PubMed
  Rooman M.J., Rodriguez J. and Wodak S.J.
  Relations between protein sequence and structure and their significance.
  J.Mol.Biol. 213, 337-350.
• PubMed
  Rooman M.J., Rodriguez J. and Wodak S.J.
  Automatic definition of recurrent local structure motifs in proteins.
  J.Mol.Biol. 213, 327-336.

1989

• PubMed
  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.
• 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.
• Wodak S.J. and Van Montagu M.
  Industrial and Agricultural Applications.
  Special issue of Biotech, March 1989, 72-76.
• PubMed
  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.

1988

• PubMed
  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.
• PubMed
  Rooman M.J. and Wodak S.J.
  Identification of predictive sequence motifs limited by protein structure database size.
  Nature 335, 45-49
• PubMed
  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
• 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.
• PubMed
  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.
• 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.
• 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