Publications

Found 56 results
Filters: Keyword is Models, Molecular and Author is Shoshana J Wodak  [Clear All Filters]
2015
Mackinnon, S. S., and S. J. Wodak, "Landscape of intertwined associations in multi-domain homo-oligomeric proteins.", J Mol Biol, vol. 427, issue 2, pp. 350-70, 2015 Jan 30.
2014
Lensink, M. F., I. H. Moal, P. A. Bates, P. L. Kastritis, A. S. J. Melquiond, E. Karaca, C. Schmitz, M. van Dijk, A. M. J. J. Bonvin, M. Eisenstein, et al., "Blind prediction of interfacial water positions in CAPRI.", Proteins, vol. 82, issue 4, pp. 620-32, 2014 Apr.
Lensink, M. F., and S. J. Wodak, "Score_set: a CAPRI benchmark for scoring protein complexes.", Proteins, vol. 82, issue 11, pp. 3163-9, 2014 Nov.
2013
Mackinnon, S. S., A. Malevanets, and S. J. Wodak, "Intertwined associations in structures of homooligomeric proteins.", Structure, vol. 21, issue 4, pp. 638-49, 2013 Apr 2.
2011
Fleishman, S. J., T. A. Whitehead, E-M. Strauch, J. E. Corn, S. Qin, H-X. Zhou, J. C. Mitchell, O. N. A. Demerdash, M. Takeda-Shitaka, G. Terashi, et al., "Community-wide assessment of protein-interface modeling suggests improvements to design methodology.", J Mol Biol, vol. 414, issue 2, pp. 289-302, 2011 Nov 25.
Malevanets, A., and S. J. Wodak, "Multiple replica repulsion technique for efficient conformational sampling of biological systems.", Biophys J, vol. 101, issue 4, pp. 951-60, 2011 Aug 17.
2010
Lensink, M. F., and S. J. Wodak, "Blind predictions of protein interfaces by docking calculations in CAPRI.", Proteins, vol. 78, issue 15, pp. 3085-95, 2010 Nov 15.
Lensink, M. F., and S. J. Wodak, "Docking and scoring protein interactions: CAPRI 2009.", Proteins, vol. 78, issue 15, pp. 3073-84, 2010 Nov 15.
2008
Sirota, F. L., S. Héry-Huynh, S. Maurer-Stroh, and S. J. Wodak, "Role of the amino acid sequence in domain swapping of the B1 domain of protein G.", Proteins, vol. 72, issue 1, pp. 88-104, 2008 Jul.
2007
Dessailly, B. H., M. F. Lensink, and S. J. Wodak, "Relating destabilizing regions to known functional sites in proteins.", BMC Bioinformatics, vol. 8, pp. 141, 2007.
2005
Méndez, R., R. Leplae, M. F. Lensink, and S. J. Wodak, "Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures.", Proteins, vol. 60, issue 2, pp. 150-69, 2005 Aug 1.
Jaramillo, A., and S. J. Wodak, "Computational protein design is a challenge for implicit solvation models.", Biophys J, vol. 88, issue 1, pp. 156-71, 2005 Jan.
2004
Wodak, S. J., and R. Méndez, "Prediction of protein-protein interactions: the CAPRI experiment, its evaluation and implications.", Curr Opin Struct Biol, vol. 14, issue 2, pp. 242-9, 2004 Apr.
Giraldo, J., L. De Maria, and S. J. Wodak, "Shift in nucleotide conformational equilibrium contributes to increased rate of catalysis of GpAp versus GpA in barnase.", Proteins, vol. 56, issue 2, pp. 261-76, 2004 Aug 1.
2003
Méndez, R., R. Leplae, L. De Maria, and S. J. Wodak, "Assessment of blind predictions of protein-protein interactions: current status of docking methods.", Proteins, vol. 52, issue 1, pp. 51-67, 2003 Jul 1.
Janin, J., K. Henrick, J. Moult, L. Ten Eyck, M. J. E. Sternberg, S. Vajda, I. Vakser, and S. J. Wodak, "CAPRI: a Critical Assessment of PRedicted Interactions.", Proteins, vol. 52, issue 1, pp. 2-9, 2003 Jul 1.
Wernisch, L., and S. J. Wodak, "Identifying structural domains in proteins.", Methods Biochem Anal, vol. 44, pp. 365-85, 2003.
2002
Ochagavia, M. Elena, J. Richelle, and S. J. Wodak, "Advanced pairwise structure alignments of proteins and analysis of conformational changes.", Bioinformatics, vol. 18, issue 4, pp. 637-40, 2002 Apr.
Ogata, K., and S. J. Wodak, "Conserved water molecules in MHC class-I molecules and their putative structural and functional roles.", Protein Eng, vol. 15, issue 8, pp. 697-705, 2002 Aug.
Janin, J., and S. J. Wodak, "Protein modules and protein-protein interaction. Introduction.", Adv Protein Chem, vol. 61, pp. 1-8, 2002.
Wodak, S. J., and J. Janin, "Structural basis of macromolecular recognition.", Adv Protein Chem, vol. 61, pp. 9-73, 2002.
2001
Jaramillo, A., L. Wernisch, S. Hery, and S. J. Wodak, "Automatic procedures for protein design.", Comb Chem High Throughput Screen, vol. 4, issue 8, pp. 643-59, 2001 Dec.
Das, U., S. Chen, M. Fuxreiter, A. A. Vaguine, J. Richelle, H. M. Berman, and S. J. Wodak, "Checking nucleic acid crystal structures.", Acta Crystallogr D Biol Crystallogr, vol. 57, issue Pt 6, pp. 813-28, 2001 Jun.
Govaerts, C., A. Lefort, S. Costagliola, S. J. Wodak, J. A. Ballesteros, J. Van Sande, L. Pardo, and G. Vassart, "A conserved Asn in transmembrane helix 7 is an on/off switch in the activation of the thyrotropin receptor.", J Biol Chem, vol. 276, issue 25, pp. 22991-9, 2001 Jun 22.
Martins, J. C., M. Enassar, R. Willem, J. M. Wieruzeski, G. Lippens, and S. J. Wodak, "Solution structure of the main alpha-amylase inhibitor from amaranth seeds.", Eur J Biochem, vol. 268, issue 8, pp. 2379-89, 2001 Apr.

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