Publications
Found 31 results
Filters: Keyword is Computer Simulation and Author is Shoshana J Wodak [Clear All Filters]
"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.
"Multiple replica repulsion technique for efficient conformational sampling of biological systems.",
Biophys J, vol. 101, issue 4, pp. 951-60, 2011 Aug 17.
"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.
"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.
"Docking and scoring protein complexes: CAPRI 3rd Edition.",
Proteins, vol. 69, issue 4, pp. 704-18, 2007 Dec 1.
"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.
"Identifying functional modules in the physical interactome of Saccharomyces cerevisiae.",
Proteomics, vol. 7, issue 6, pp. 944-60, 2007 Mar.
"Relating destabilizing regions to known functional sites in proteins.",
BMC Bioinformatics, vol. 8, pp. 141, 2007.
"GenePro: a Cytoscape plug-in for advanced visualization and analysis of interaction networks.",
Bioinformatics, vol. 22, issue 17, pp. 2178-9, 2006 Sep 1.
"Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures.",
Proteins, vol. 60, issue 2, pp. 150-69, 2005 Aug 1.
"Computational protein design is a challenge for implicit solvation models.",
Biophys J, vol. 88, issue 1, pp. 156-71, 2005 Jan.
"Combining pattern discovery and discriminant analysis to predict gene co-regulation.",
Bioinformatics, vol. 20, issue 15, pp. 2370-9, 2004 Oct 12.
"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.
"Identifying structural domains in proteins.",
Methods Biochem Anal, vol. 44, pp. 365-85, 2003.
"An overview of data models for the analysis of biochemical pathways.",
Brief Bioinform, vol. 4, issue 3, pp. 246-59, 2003 Sep.
"Structural basis of macromolecular recognition.",
Adv Protein Chem, vol. 61, pp. 9-73, 2002.
"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.
"Pathways of ligand clearance in acetylcholinesterase by multiple copy sampling.",
J Mol Biol, vol. 298, issue 4, pp. 705-26, 2000 May 12.
"Representing and analysing molecular and cellular function using the computer.",
Biol Chem, vol. 381, issue 9-10, pp. 921-35, 2000 Sep-Oct.
"Structural features of protein-nucleic acid recognition sites.",
Biochemistry, vol. 38, issue 7, pp. 1999-2017, 1999 Feb 16.
"Unfolding simulations of the 85-102 beta-hairpin of barnase.",
J Mol Biol, vol. 251, issue 3, pp. 432-47, 1995 Aug 18.
"The quaternary structure of carbonmonoxy hemoglobin ypsilanti.",
Proteins, vol. 15, issue 1, pp. 1-4, 1993 Jan.
"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.
"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.
"The design of idealized alpha/beta-barrels: analysis of beta-sheet closure requirements.",
Proteins, vol. 7, issue 3, pp. 249-56, 1990.