Publications
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2006. Hydrogen-bonding patterns of cholesterol in lipid membranes. Chem. Phys. Lett.. 425:329–335.
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2006. Identification of two critical residues within the Cys-loop sequence that determine fast-gating kinetics in a pentameric ligand-gated ion channel. J. Mol. Neurosci.. 30:63–64.
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2006. Implications of the quaternary twist allosteric model for the physiology and pathology of nicotinic acetylcholine receptors. Proc. Natl. Acad. Sci. U.s.a.. 103:16965–16970.
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2006. An Immersive Visualization and Interaction Paradigm for Genomic Databases Exploration. Mediterranean Journal of Computers and Networks. 2:118–124.
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2006. Impact of the mutation A21G (Flemish variant) on Alzheimer’s beta-amyloid dimers by molecular dynamics simulations. Biophys. J.. 91:3829–3840.
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2006. Implications of the quaternary twist allosteric model for the physiology and pathology of nicotinic acetylcholine receptors. Proceedings of the National Academy of Sciences. 103:16965–16970.
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2006. Improved Wang-Landau sampling through the use of smoothed potential-energy surfaces. J. Chem. Phys.. 124
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2006. Investigating the local flexibility of functional residues in hemoproteins. Biophys. J.. 90:2706–2717.
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2006. Mapping a Homopolymer onto a Model Fluid. J. Chem. Phys.. 125:064906.
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2006. Molecular modeling and simulation of water near model micelles: diffusion, rotational relaxation and structure at the hydration interface. J. Phys. Chem. B. 110:11504–10.
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2006. Nonequilibrium molecular dynamics simulation of a photoswitchable peptide. Chem. Phys.. 323:36–44.
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2006. Normal mode analysis as a prerequisite for drug design: Application to matrix metalloproteinases inhibitors. Febs Lett.. 580:5130–5136.
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2006. Odorant Binding and Conformational Dynamics in the Odorant-binding Protein. J. Biol. Chem.. 281:29929–29937.
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2006. Photoinduced conformational dynamics of a photoswitchable peptide: A nonequilibrium molecular dynamics simulation study. Biophys. J.. 91:1224–1234.
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2006. PHYS 4-Applications of activated methods to proteins and materials science. Abstracts of Papers of the American Chemical Society. 232
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2006. Probing a model of a GPCR/ligand complex in an explicit membrane environment: The human cholecystokinin-1 receptor. Biophys. J.. 90:1232–1240.
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2006. Protein Peeling 2: a web server to convert protein structures into series of protein units. Nucleic Acids Res.. 34:W75-W78.
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2006. `Protein Peeling': an approach for splitting a 3D protein structure into compact fragments. Bioinformatics. 22:129–133.
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2006. Structural changes of region 1-16 of the Alzheimer disease amyloid beta-peptide upon zinc binding and in vitro aging. J. Biol. Chem.. 281:2151–2161.
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2006. Structure and dynamics of hydrogen bonds in the interface of a C12E6 spherical micelle in water solution: a MD study at various temperatures. J. Phys. Chem. B. 110:18254–61.
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2006. Structures of soluble amyloid oligomers from computer simulations. Proteins: Struct., Funct., Bioinf.. 65:180–191.
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2006. Visual Mining for Microarray Knowledge Discovery. International Conference on Information & Communication Technologies: from Theory to Applications (ICTTA 2006 - IEEE).
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2006. Water percolation governs polymorphic transitions and conductivity of DNA. Phys. Rev. Lett.. 97:137801.
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2006. Yeast Naked DNA Spatial Organization Predisposes to Transcriptional Regulation. International Conference on Computational Science and its Applications (ICCSA 2006). 3984:222–231.
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2007. Atomistic modeling of the membrane-embedded synaptic fusion complex: a grand challenge project on the DEISA HPC infrastructure. ParCo 2007, Parallel Computing: Architectures, Algorithms and Applications. 38:729–736.