Publications
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2005. Electrostatic polymer condensation and the A/B polymorphism in DNA: Sequence effects. J. Chem. Theory Comput.. 1:325–336.
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2005. Energy landscape of a small peptide revealed by dihedral angle principal component analysis. Proteins: Struct., Funct., Bioinf.. 58:45–52.
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2005. EvDTree: structure-dependent substitution profiles based on decision tree classification of 3D environments. Bmc Bioinf.. 6
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2005. Exploring the early steps of amyloid peptide aggregation by computers. Acc. Chem. Res.. 38:885–891.
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2005. Exploring the free energy landscape of a short peptide using an average force. J. Chem. Phys.. 123:244906.
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2005. Following the aggregation of amyloid-forming peptides by computer simulations. J. Chem. Phys.. 122:174904.
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2005. Following the aggregation of amyloid-forming peptides by computer simulations.. Abstracts of Papers of the American Chemical Society. 229:U735.
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2005. Free energy landscape and folding mechanism of a beta-hairpin in explicit water: A replica exchange molecular dynamics study. Proteins: Struct., Funct., Bioinf.. 61:795–808.
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2005. Hydration and thermodynamic equilibrium of non-ionic surfactant in solution. Coll Surf A. 261:93–99.
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2005. Immersive graph-based visualization and exploration of biological data relationships. Data Sci. J.. 4:189–194.
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2005. Improved greedy algorithm for protein structure reconstruction. J. Comput. Chem.. 26:506–513.
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2005. Insights into the recognition and association of transmembrane $\alpha$-helices. The free energy of $\alpha$-helix dimerization in glycophorin A. J. Am. Chem. Soc.. 127:8478–8484.
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2005. Molecular tuning of fast gating in pentameric ligand-gated ion channels. Proc. Natl. Acad. Sci. U.s.a.. 102:18207–18212.
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2005. Membrane protein structure quality in molecular dynamics simulation. Journal of Molecular Graphics \& Modelling. 24:157–165.
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2005. Modular RNA architecture revealed by computational analysis of existing pseudoknots and ribosomal RNAs. Nuc. Acids Res.. 33:1384–1398.
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2005. Normal mode analysis suggests a quaternary twist model for the nicotinic receptor gating mechanism. Biophys. J.. 88:3954–3965.
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2005. Navigation and analysis of the energy landscape of small proteins using the activation-relaxation technique. Phys. Biol.. 2:S101-S107.
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2005. Structure and energy landscape of a photoswitchable peptide: A replica exchange molecular dynamics study. Proteins: Struct., Funct., Bioinf.. 60:485–494.
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2005. Visual data mining of genomic databases by immersive graph-based exploration. international Conference on Computer Graphics and interactive Techniques in Australasia and South East Asia (GRAPHITE 2005 - ACM-ACMSIGRAPH Sponsored). :143–146.
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2004. The antitumor properties of the alpha 3(IV)-(185-203) peptide from the NC1 domain of type IV collagen (tumstatin) are conformation-dependent. J. Biol. Chem.. 279:2091–2100.
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2004. Combining Applications and Databases Integration Approaches in a Common Distributed Genomic Platform. International CODATA Conference, The Information Society: New Horizons for Science.
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2004. Complex folding pathways in a simple beta-hairpin. Proteins: Struct., Funct., Bioinf.. 56:464–474.
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2004. Conformational sampling and dynamics of membrane proteins from 10-nanosecond computer simulations. Proteins: Struct., Funct., Bioinf.. 57:783–791.
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2004. Conformational transitions in proteins and membranes. Novel Approaches to the Structure and Dynamics of Liquids: Experiments, Theories and Simulations. :485–502.
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2004. Critical role of the C-terminal segment in the maturation and export to the cell surface of the homopentameric $\alpha$7–5HT3A receptor. Eur. J. Neurosci.. 20:2022–2030.