Publications

Found 22 results
Filters: Keyword is Software and Author is Shoshana J Wodak  [Clear All Filters]
2013
Lensink, M. F., and S. J. Wodak, "Docking, scoring, and affinity prediction in CAPRI.", Proteins, vol. 81, issue 12, pp. 2082-95, 2013 Dec.
2012
Fiume, M., E. J. M. Smith, A. Brook, D. Strbenac, B. Turner, A. M. Mezlini, M. D. Robinson, S. J. Wodak, and M. Brudno, "Savant Genome Browser 2: visualization and analysis for population-scale genomics.", Nucleic Acids Res, vol. 40, issue Web Server issue, pp. W615-21, 2012 Jul.
2011
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.
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
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
Leplae, R., A. Hebrant, S. J. Wodak, and A. Toussaint, "ACLAME: a CLAssification of Mobile genetic Elements.", Nucleic Acids Res, vol. 32, issue Database issue, pp. D45-9, 2004 Jan 1.
2003
Wernisch, L., and S. J. Wodak, "Identifying structural domains in proteins.", Methods Biochem Anal, vol. 44, pp. 365-85, 2003.
2002
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.
2001
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.
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.
1999
Vaguine, A. A., J. Richelle, and S. J. Wodak, "SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model.", Acta Crystallogr D Biol Crystallogr, vol. 55, issue Pt 1, pp. 191-205, 1999 Jan.
1996
Pontius, J., J. Richelle, and S. J. Wodak, "Deviations from standard atomic volumes as a quality measure for protein crystal structures.", J Mol Biol, vol. 264, issue 1, pp. 121-36, 1996 Nov 22.
1994
Pintar, A., A. Chollet, C. Bradshaw, A. Chaffotte, C. Cadieux, M. J. Rooman, K. Hallenga, J. Knowles, M. Goldberg, and S. J. Wodak, "Conformational properties of four peptides corresponding to alpha-helical regions of Rhodospirillum cytochrome c2 and bovine calcium binding protein.", Biochemistry, vol. 33, issue 37, pp. 11158-73, 1994 Sep 20.
Cerf, C., G. Lippens, V. Ramakrishnan, S. Muyldermans, A. Segers, L. Wyns, S. J. Wodak, and K. Hallenga, "Homo- and heteronuclear two-dimensional NMR studies of the globular domain of histone H1: full assignment, tertiary structure, and comparison with the globular domain of histone H5.", Biochemistry, vol. 33, issue 37, pp. 11079-86, 1994 Sep 20.
1991
Huysmans, M., J. Richelle, and S. J. Wodak, "SESAM: a relational database for structure and sequence of macromolecules.", Proteins, vol. 11, issue 1, pp. 59-76, 1991.
1990
Lasters, I., S. J. Wodak, and F. Pio, "The design of idealized alpha/beta-barrels: analysis of beta-sheet closure requirements.", Proteins, vol. 7, issue 3, pp. 249-56, 1990.