Publications
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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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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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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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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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2012. Distinct Dimerization for Various Alloforms of the Amyloid-Beta Protein: A beta(1-40), A beta(1-42), and A beta(1-40)(D23N). J. Phys. Chem. B. 116:4043–4055.
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2011. Distinct Morphologies for Amyloid Beta Protein Monomer: A beta(1-40), A beta(1-42), and A beta(1-40)(D23N). J. Chem. Theory Comput.. 7:2584–2592.
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2015. Epock: rapid analysis of protein pocket dynamics. Bioinformatics. 31:1478–1480.
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2004. Early steps of amyloid-petide oligomerisation explored by simulations. Neurobiol. Aging. 25:S143.
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2014. Effect of the English Familial Disease Mutation (H6R) on the Monomers and Dimers of A beta 40 and A beta 42. Acs Chem. Neurosci.. 5:646–657.
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2013. Effect of the Tottori Familial Disease Mutation (D7N) on the Monomers and Dimers of A beta(40) and A beta(42). Acs Chem. Neurosci.. 4:1446–1457.
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1991. EFFECT OF UREY-BRADLEY-SHIMANOUCHI FORCE-FIELD ON THE HARMONIC DYNAMICS OF PROTEINS. Proteins-structure Function and Genetics. 11:120–132.
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2011. Effects of all-atom force fields on amyloid oligomerization: replica exchange molecular dynamics simulations of the A beta(16-22) dimer and trimer. Phys. Chem. Chem. Phys.. 13:9778–9788.
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2019. Effects of all-atom molecular mechanics force fields on amyloid peptide assembly: the case of aβ16–22 dimer. Journal of chemical theory and computation. 15:1440–1452.
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2011. Effects of G33A and G33I Mutations on the Structures of Monomer and Dimer of the Amyloid-beta Fragment 29-42 by Replica Exchange Molecular Dynamics Simulations. J. Phys. Chem. B. 115:1282–1288.
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2010. Effects of the RGTFEGKF Inhibitor on the Structures of the Transmembrane Fragment 70-86 of Glycophorin A: An All-Atom Molecular Dynamics Study. J. Phys. Chem. B. 114:1004–1009.
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2016. Electrostatics analysis of the mutational and pH effects of the N-terminal domain self-association of the major ampullate spidroin. Soft Matter. 12:5600–5612.
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2009. Energy Flow and Long-Range Correlations in Guanine-Binding Riboswitch: A Nonequilibrium Molecular Dynamics Study. J. Phys. Chem. B. 113:9340–9347.
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2008. Energy landscapes of the monomer and dimer of the Alzheimer's peptide A beta(1-28). J. Chem. Phys.. 128:125108.
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2016. Evaluation of the coarse-grained OPEP force field for protein-protein docking. Bmc Biophysics. 9
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2001. Evidence that the 127-164 region of prion proteins has two equi-energetic conformations with beta or alpha features. Biophys. J.. 81:1657–1665.
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2009. Exploring amyloid aggregates with the OPEP coarse-grained force field. Abstracts of Papers of the American Chemical Society. 238
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2008. Exploring energy landscapes of protein folding and aggregation. Front. Biosci.. 13:4495–4516.
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2004. Exploring the early steps of aggregation of amyloid-forming peptide KFFE. Journal of Physics-condensed Matter. 16:S5047-S5054.
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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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2002. Exploring the energy landscape of proteins: A characterization of the activation-relaxation technique. J. Chem. Phys.. 117:11379–11387.