Publications
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2016. Dimerization Mechanism of Alzheimer A beta(40) Peptides: The High Content of Intrapeptide-Stabilized Conformations in A2V and A2T Heterozygous Dimers Retards Amyloid Fibril Formation. J. Phys. Chem. B. 120:12111–12126.
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2007. Dihedral angle principal component analysis of molecular dynamics simulations. J. Chem. Phys.. 126
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1997. A diffusion process-controlled Monte Carlo method for finding the global energy minimum of a polypeptide chain .1. Formulation and test on a hexadecapeptide. J. Chem. Phys.. 106:5260–5270.
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2008. Diffusion of glycerol through Escherichia coli aquaglyceroporin GlpF. Biophys. J.. 94:832–839.
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2002. Differential core histone binding behavior: RNA polymerase I promoter region vs 5S rDNA positioning DNA sequences. Cell Biochem. Biophys.. 37:1–13.
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2017. Determinants of neuroglobin plasticity highlighted by joint coarse-grained simulations and high pressure crystallography. Sci Rep. 7:1858.
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2019. Design games and game design: Relations between design, codesign and serious games in adult education. From UXD to LivXD: Living eXperience Design. :229–253.
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2022. Design – a new way to look at old molecules. Journal of Integrative Bioinformatics. 19:20220020.
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1991. Derivation and testing of explicit equations of motion for polymers described by internal coordinates. J. Comput. Phys.. 92:261–272.
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2005. Dependency between consecutive local conformations helps assemble protein structures from secondary structures using Go potential and greedy algorithm. Proteins: Struct., Funct., Bioinf.. 61:732–740.
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2000. Dependence of NMR isotropic shift averages and nuclear shielding tensors on the internal rotation of the functional group X about the C-X bond in seven simple vinylic derivatives H2C=CH-X. Mol. Phys.. 98:329–342.
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2013. Density functional conformational study of 2-O-sulfated 3,6 anhydro-alpha-D-galactose and of neo-kappa- and iota-carrabiose molecules in gas phase and water. J. Mol. Model.. 19:893–904.
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2012. Delivering the native structures of peptides from computer simulations and predicted NMR proton chemical shifts. J. Pept. Sci.. 18:S38.
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2009. Deforming DNA: from physics to biology. Chemphyschem. 10:1399–404.
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2007. Docking of alpha-cobratoxin suggests a basal conformation of the nicotinic receptor. Biochem. Biophys. Res. Commun.. 359:413–418.
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2010. DNA structures from phosphate chemical shifts. Nucleic Acids Res.. 38:e18.
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1999. DNA structure and polymerase fidelity. J. Mol. Biol.. 293:835–853.
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1994. DNA self-fitting: the double helix directs the geometry of its supramolecular assembly. Embo J.. 13:2737–2746.
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1998. DNA crossovers and type II DNA topoisomerases: A thermodynamical study. J. Mol. Biol.. 284:1279–1287.
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2011. Discrimination of agonists versus antagonists of nicotinic ligands based on docking onto AChBP structures. J. Mol. Graph. Model.. 30:100–109.
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2019. C-Terminal Plays as the Possible Nucleation of the Self-Aggregation of the S-Shape Aβ Tetramer in Solution: Intensive MD Study.. ACS Omega. 4(6):11066-11073.
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2004. The C-terminal domain of Escherichia coli Hfq increases the stability of the hexamer. Eur. J. Biochem.. 271:1258–1265.
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2017. Critical structural fluctuations of proteins upon thermal unfolding challenge the Lindemann criterion. Proc Natl Acad Sci U S A. 114:9361-9366.
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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.
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2014. A cooperative mechanism of clotrimazoles in P450 revealed by the dissociation picture of clotrimazole from P450. J. Chem. Inf. Model.. 54:1218–1225.