Publications

Found 30 results
Filters: Keyword is Algorithms and Author is Shoshana J Wodak  [Clear All Filters]
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.
Qiao, W., W. Wang, E. Laurenti, A. L. Turinsky, S. J. Wodak, G. D. Bader, J. E. Dick, and P. W. Zandstra, "Intercellular network structure and regulatory motifs in the human hematopoietic system.", Mol Syst Biol, vol. 10, pp. 741, 2014 Jul 15.
2013
Moretti, R., S. J. Fleishman, R. Agius, M. Torchala, P. A. Bates, P. L. Kastritis, J. P. G. L. M. Rodrigues, M. Trellet, A. M. J. J. Bonvin, M. Cui, et al., "Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions.", Proteins, vol. 81, issue 11, pp. 1980-7, 2013 Nov.
2011
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.
2009
Vlasblom, J., and S. J. Wodak, "Markov clustering versus affinity propagation for the partitioning of protein interaction graphs.", BMC Bioinformatics, vol. 10, pp. 99, 2009.
2008
Pu, S., K. Ronen, J. Vlasblom, J. Greenblatt, and S. J. Wodak, "Local coherence in genetic interaction patterns reveals prevalent functional versatility.", Bioinformatics, vol. 24, issue 20, pp. 2376-83, 2008 Oct 15.
2007
Lensink, M. F., R. Méndez, and S. J. Wodak, "Docking and scoring protein complexes: CAPRI 3rd Edition.", Proteins, vol. 69, issue 4, pp. 704-18, 2007 Dec 1.
Wodak, S. J., "From the Mediterranean coast to the shores of Lake Ontario: CAPRI's premiere on the American continent.", Proteins, vol. 69, issue 4, pp. 697-8, 2007 Dec 1.
Pu, S., J. Vlasblom, A. Emili, J. Greenblatt, and S. J. Wodak, "Identifying functional modules in the physical interactome of Saccharomyces cerevisiae.", Proteomics, vol. 7, issue 6, pp. 944-60, 2007 Mar.
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.
2006
Vlasblom, J., S. Wu, S. Pu, M. Superina, G. Liu, C. Orsi, and S. J. Wodak, "GenePro: a Cytoscape plug-in for advanced visualization and analysis of interaction networks.", Bioinformatics, vol. 22, issue 17, pp. 2178-9, 2006 Sep 1.
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.
Croes, D., F. Couche, S. J. Wodak, and J. van Helden, "Metabolic PathFinding: inferring relevant pathways in biochemical networks.", Nucleic Acids Res, vol. 33, issue Web Server issue, pp. W326-30, 2005 Jul 1.
2004
Simonis, N., S. J. Wodak, G. N. Cohen, and J. van Helden, "Combining pattern discovery and discriminant analysis to predict gene co-regulation.", Bioinformatics, vol. 20, issue 15, pp. 2370-9, 2004 Oct 12.
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.
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.
van Helden, J., L. Wernisch, D. Gilbert, and S. J. Wodak, "Graph-based analysis of metabolic networks.", Ernst Schering Res Found Workshop, issue 38, pp. 245-74, 2002.
Wodak, S. J., and J. Janin, "Structural basis of macromolecular recognition.", Adv Protein Chem, vol. 61, pp. 9-73, 2002.
2000
Wernisch, L., S. Hery, and S. J. Wodak, "Automatic protein design with all atom force-fields by exact and heuristic optimization.", J Mol Biol, vol. 301, issue 3, pp. 713-36, 2000 Aug 18.

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