Browsing by Subject "Molecular dynamics simulations"

Article

Amyloid-like self-assembly of a dodecapeptide sequence from the adenovirus fiber shaft: Perspectives from molecular dynamics simulations

Tamamis, Phanourios; Archontis, Georgios Z. (2011)

Peptide and protein self-assembly is related to the fundamental problems of protein folding and misfolding and has potential applications in medicine, materials science and nanotechnology. Sequence repeats from self-assembling ...

Article

Amyloid-like self-assembly of peptide sequences from the adenovirus fiber shaft: Insights from molecular dynamics simulations

Tamamis, Phanourios; Kasotakis, E.; Mitraki, A.; Archontis, Georgios Z. (2009)

The self-assembly of peptides and proteins into nanostructures is related to the fundamental problems of protein folding and misfolding and has potential applications in medicine, materials science and nanotechnology. ...

Article

Analysis of depolarization ratios of ClNO2 dissolved in methanol

Trimithioti, Marilena; Akimov, A. V.; Prezhdo, O. V.; Hayes, Sophia C. (2014)

A detailed analysis of the resonance Raman depolarization ratio dispersion curve for the N-O symmetric stretch of nitryl chloride in methanol at excitation wavelengths spanning the D absorption band is presented. The ...

Article

Computational design of novel fullerene analogues as potential HIV-1 PR inhibitors: Analysis of the binding interactions between fullerene inhibitors and HIV-1 PR residues using 3D QSAR, molecular docking and molecular dynamics simulations

Durdagi, S.; Mavromoustakos, Thomas M.; Chronakis, Nikos; Papadopoulos, Manthos G. (2008)

A series of experimentally reported as well as computationally designed monoadducts and bisadducts of [60]fullerene analogues have been used in order to analyze the binding interactions between fullerene based inhibitors ...

Article

Computational protein design with a generalized born solvent model: Application to asparaginyl-tRNA synthetase

Polydorides, Savvas; Amara, Najette; Aubard, C.; Plateau, P.; Simonson, T.; Archontis, Georgios Z. (2011)

Computational Protein Design (CPD) is a promising method for high throughput protein and ligand mutagenesis. Recently, we developed a CPD method that used a polar-hydrogen energy function for protein interactions and a ...

Article

Conformational analysis of compstatin analogues with molecular dynamics simulations in explicit water

Tamamis, Phanourios; Skourtis, Spiros S.; Morikis, D.; Lambris, J. D.; Archontis, Georgios Z. (2007)

The cyclic 13-residue peptide compstatin is a potential therapeutic agent against the unregulated activation of the complement system. A thorough knowledge of its structural and dynamical properties in solution may assist ...

Article

Glycogen phosphorylase inhibitors: A free energy perturbation analysis of glucopyranose spirohydantoin analogues

Archontis, Georgios Z.; Watson, K. A.; Xie, Q.; Andreou, Georgia; Chrysina, Evangelia D.; Zographos, Spyros E.; Oikonomakos, Nikos G.; Karplus, M. (2005)

GP catalyzes the phosphorylation of glycogen to Glc-1-P. Because of its fundamental role in the metabolism of glycogen, GP has been the target for a systematic structure-assisted design of inhibitory compounds, which could ...

Article

Helix formation by alanine-based peptides in pure water and electrolyte solutions: Insights from molecular dynamics simulations

Ioannou, F.; Leontidis, Epameinondas; Archontis, Georgios Z. (2013)

Specific ion effects on oligopeptide conformations in solution are attracting strong research attention, because of their impact on the protein-folding problem and on several important biological-biotechnological applications. ...

Article

Helix formation by alanine-based peptides in pure water and electrolyte solutions: Insights from molecular dynamics simulationsAAA

Ioannou, F.; Leontidis, Epameinondas; Archontis, Georgios Z. (2013)

Specific ion effects on oligopeptide conformations in solution are attracting strong research attention, because of their impact on the protein-folding problem and on several important biological-biotechnological applications. ...

Article

Liquid expanded monolayers of lipids as model systems to understand the anionic hofmeister series: 2. Ion partitioning is mostly a matter of size

Leontidis, Epameinondas; Aroti, Andria (2009)

In the preceding paper of this series [Leontidis, E.

Article

Self-assembly of an aspartate-rich sequence from the adenovirus fiber shaft: Insights from molecular dynamics simulations and experiments

Tamamis, Phanourios; Terzaki, K.; Kassinopoulos, Marios; Mastrogiannis, L.; Mossou, E.; Forsyth, V. T.; Mitchell, E. P.; Mitraki, A.; Archontis, Georgios Z. (2014)

The self-assembly of short peptides into fibrous nanostructures (such as fibrils and tubes) has recently become the subject of intense theoretical and experimental scrutiny, as such assemblies are promising candidates for ...

Article

Species specificity of the complement inhibitor compstatin investigated by all-atom molecular dynamics simulations

Tamamis, Phanourios; Morikis, D.; Floudas, C. A.; Archontis, Georgios Z. (2010)

The development of compounds to regulate the activation of the complement system in non-primate species is of profound interest because it can provide models for human diseases. The peptide compstatin inhibits protein C3 ...

Article

Wetting of doped carbon nanotubes by water droplets

Kotsalis, E. M.; Demosthenous, E.; Walther, J. H.; Kassinos, Stavros C.; Koumoutsakos, P. (2005)

We study the wetting of doped single- and multi-walled carbon nanotubes by water droplets using molecular dynamics simulations. Chemisorbed hydrogen is considered as a model of surface impurities. We study systems with ...