Publications

Found 21 results
Filters: Keyword is Databases, Protein and Author is Shoshana J Wodak  [Clear All Filters]
2015
Pu, S., J. Vlasblom, A. Turinsky, E. Marcon, S. Phanse, S. Smiley Trimble, J. Olsen, J. Greenblatt, A. Emili, and S. J. Wodak, "Extracting high confidence protein interactions from affinity purification data: at the crossroads.", J Proteomics, vol. 118, pp. 63-80, 2015 Apr 06.
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
Turinsky, A. L., S. Razick, B. Turner, I. M. Donaldson, and S. J. Wodak, "Navigating the global protein-protein interaction landscape using iRefWeb.", Methods Mol Biol, vol. 1091, pp. 315-31, 2014.
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
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.
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
Wodak, S. J., J. Vlasblom, and S. Pu, "High-throughput analyses and curation of protein interactions in yeast.", Methods Mol Biol, vol. 759, pp. 381-406, 2011.
Turinsky, A. L., S. Razick, B. Turner, I. M. Donaldson, and S. J. Wodak, "Interaction databases on the same page.", Nat Biotechnol, vol. 29, issue 5, pp. 391-3, 2011 May.
Hao, Y., A. Merkoulovitch, J. Vlasblom, S. Pu, A. L. Turinsky, D. Roudeva, B. Turner, J. Greenblatt, and S. J. Wodak, "OrthoNets: simultaneous visual analysis of orthologs and their interaction neighborhoods across different organisms.", Bioinformatics, vol. 27, issue 6, pp. 883-4, 2011 Mar 15.
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.
Turner, B., S. Razick, A. L. Turinsky, J. Vlasblom, E. K. Crowdy, E. Cho, K. Morrison, I. M. Donaldson, and S. J. Wodak, "iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence.", Database (Oxford), vol. 2010, pp. baq023, 2010.
Turinsky, A. L., S. Razick, B. Turner, I. M. Donaldson, and S. J. Wodak, "Literature curation of protein interactions: measuring agreement across major public databases.", Database (Oxford), vol. 2010, pp. baq026, 2010.
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
Dessailly, B. H., M. F. Lensink, C. A. Orengo, and S. J. Wodak, "LigASite--a database of biologically relevant binding sites in proteins with known apo-structures.", Nucleic Acids Res, vol. 36, issue Database issue, pp. D667-73, 2008 Jan.
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.
2006
Simonis, N., D. Gonze, C. Orsi, J. van Helden, and S. J. Wodak, "Modularity of the transcriptional response of protein complexes in yeast.", J Mol Biol, vol. 363, issue 2, pp. 589-610, 2006 Oct 20.
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.
2002
Pajon, A., W. F. Vranken, M. Angeles Jimenez, M. Rico, and S. J. Wodak, "Pescador: the PEptides in Solution ConformAtion Database: Online Resource.", J Biomol NMR, vol. 23, issue 2, pp. 85-102, 2002 Jun.
Janin, J., and S. J. Wodak, "Protein modules and protein-protein interaction. Introduction.", Adv Protein Chem, vol. 61, pp. 1-8, 2002.