Publications

Found 31 results
Filters: Keyword is Computer Simulation and Author is Shoshana J Wodak  [Clear All Filters]
2011
Leung, E., A. Datti, M. Cossette, J. Goodreid, S. E. McCaw, M. Mah, A. Nakhamchik, K. Ogata, M. El Bakkouri, Y-Q. Cheng, et al., "Activators of cylindrical proteases as antimicrobials: identification and development of small molecule activators of ClpP protease.", Chem Biol, vol. 18, issue 9, pp. 1167-78, 2011 Sep 23.
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.
2008
Malevanets, A., F. L. Sirota, and S. J. Wodak, "Mechanism and energy landscape of domain swapping in the B1 domain of protein G.", J Mol Biol, vol. 382, issue 1, pp. 223-35, 2008 Sep 26.
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
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.
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.
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
Wernisch, L., and S. J. Wodak, "Identifying structural domains in proteins.", Methods Biochem Anal, vol. 44, pp. 365-85, 2003.
Deville, Y., D. Gilbert, J. van Helden, and S. J. Wodak, "An overview of data models for the analysis of biochemical pathways.", Brief Bioinform, vol. 4, issue 3, pp. 246-59, 2003 Sep.
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.
Van Belle, D., L. De Maria, G. Iurcu, and S. J. Wodak, "Pathways of ligand clearance in acetylcholinesterase by multiple copy sampling.", J Mol Biol, vol. 298, issue 4, pp. 705-26, 2000 May 12.
van Helden, J., A. Naim, R. Mancuso, M. Eldridge, L. Wernisch, D. Gilbert, and S. J. Wodak, "Representing and analysing molecular and cellular function using the computer.", Biol Chem, vol. 381, issue 9-10, pp. 921-35, 2000 Sep-Oct.
1999
Nadassy, K., S. J. Wodak, and J. Janin, "Structural features of protein-nucleic acid recognition sites.", Biochemistry, vol. 38, issue 7, pp. 1999-2017, 1999 Feb 16.
1995
Pugliese, L., M. Prévost, and S. J. Wodak, "Unfolding simulations of the 85-102 beta-hairpin of barnase.", J Mol Biol, vol. 251, issue 3, pp. 432-47, 1995 Aug 18.
1993
Janin, J., and S. J. Wodak, "The quaternary structure of carbonmonoxy hemoglobin ypsilanti.", Proteins, vol. 15, issue 1, pp. 1-4, 1993 Jan.
1991
Prévost, M., S. J. Wodak, B. Tidor, and M. Karplus, "Contribution of the hydrophobic effect to protein stability: analysis based on simulations of the Ile-96----Ala mutation in barnase.", Proc Natl Acad Sci U S A, vol. 88, issue 23, pp. 10880-4, 1991 Dec 1.
Rooman, M. J., J. P. Kocher, and S. J. Wodak, "Prediction of protein backbone conformation based on seven structure assignments. Influence of local interactions.", J Mol Biol, vol. 221, issue 3, pp. 961-79, 1991 Oct 5.
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.

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