Browsing by Subject "Models, Molecular"

Article

The 1.76 Å resolution crystal structure of glycogen phosphorylase b complexed with glucose, and CP320626, a potential antidiabetic drug

Oikonomakos, Nikos G.; Zographos, Spyros E.; Skamnaki, Vicky T.; Archontis, Georgios Z. (2002)

CP320626, a potential antidiabetic drug, inhibits glycogen phosphorylase in synergism with glucose. To elucidate the structural basis of synergistic inhibition, we determined the structure of muscle glycogen phosphorylase ...

Article

A novel QSPR model for predicting θ (lower critical solution temperature) in polymer solutions using molecular descriptors

Melagraki, G.; Afantitis, Antreas; Sarimveis, H.; Koutentis, Panayiotis Andreas; Markopoulos, J.; Igglessi-Markopoulou, O. (2007)

In this study, we present a new model that has been developed for the prediction of θ, (lower critical solution temperature) using a database of 169 data points that include 12 polymers and 67 solvents. For the characterization ...

Article

Aerial Oxidation of a VIV-Iminopyridine Hydroquinonate Complex: A Trap for the VIV-Semiquinonate Radical Intermediate

Stylianou, Marios; Drouza, Chryssoula; Giapintzakis, Ioannis; Athanasopoulos, Georgios I.; Keramidas, Anastasios D. (2015)

The reaction of 2,5-bis[N,N′-bis(2-pyridyl-aminomethyl)aminomethyl]-p-hydroquinone (H2bpymah) with VO2+ salts in acetonitrile or water at a low pH (2.2-3.5) results in the isolation of [{VIV(O)(Cl)}2(μ-bpymah)], the ...

Article

Amphiphilic model conetworks based on cross-linked star copolymers of benzyl methacrylate and 2-(dimenthylamino)ethyl methacrylate: Synthesis, characterization, and DNA adsorption studies

Achilleos, Demetra S.; Georgiou, Theoni K.; Patrickios, Costas S. (2006)

Six amphiphilic model conetworks of a new structure, that of cross-linked "in-out" star copolymers, were synthesized by the group transfer polymerization (GTP) of the hydrophobic monomer benzyl methacrylate (BzMA) and the ...

Article

Analysis of binding parameters of HIV-1 integrase inhibitors: Correlates of drug inhibition and resistance

Loizidou, Eriketi Z.; Zeinalipour-Yazdi, Constantinos D.; Christofides, Tasos C.; Kostrikis, Leontios G. (2009)

This study undertook an exploratory data analysis of the binding parameters of HIV-1 integrase inhibitors. The study group involved inhibitors in preclinical development from the diketo acid, pyrroloquinoline and naphthyridine ...

Article

Analysis of binding parameters of HIV-1 integrase inhibitors: Correlates of drug inhibition and resistance

Loizidou, Eriketi Z.; Zeinalipour-Yazdi, Constantinos D.; Christofides, Tasos C.; Kostrikis, Leontios G. (2009)

This study undertook an exploratory data analysis of the binding parameters of HIV-1 integrase inhibitors. The study group involved inhibitors in preclinical development from the diketo acid, pyrroloquinoline and naphthyridine ...

Article

Analysis of binding parameters of HIV-1 integrase inhibitors: Correlates of drug inhibition and resistance

Loizidou, Eriketi Z.; Zeinalipour-Yazdi, Constantinos D.; Christofides, Tasos C.; Kostrikis, Leontios G. (2009)

This study undertook an exploratory data analysis of the binding parameters of HIV-1 integrase inhibitors. The study group involved inhibitors in preclinical development from the diketo acid, pyrroloquinoline and naphthyridine ...

Article

Binding free energies and free energy components from molecular dynamics and Poisson-Boltzmann calculations. Application to amino acid recognition by aspartyl-tRNA synthetase

Archontis, Georgios Z.; Simonson, T.; Karplus, M. (2001)

Specific amino acid binding by aminoacyl-tRNA synthetases (aaRS) is necessary for correct translation of the genetic code. Engineering a modified specificity into aminoacyl-tRNA synthetases has been proposed as a means to ...

Article

CHARMM: The biomolecular simulation program

Brooks, B. R.; Brooks III, C. L.; Mackerell Jr., A. D.; Nilsson, L.; Petrella, R. J.; Roux, B.; Won, Y.; Archontis, Georgios Z.; Bartels, C.; Boresch, S.; Caflisch, A.; Caves, L.; Cui, Q.; Dinner, A. R.; Feig, M.; Fischer, S.; Gao, J.; Hodoscek, M.; Im, W.; Kuczera, K.; Lazaridis, T.; Ma, J.; Ovchinnikov, V.; Paci, E.; Pastor, R. W.; Post, C. B.; Pu, J. Z.; Schaefer, M.; Tidor, B.; Venable, R. M.; Woodcock, H. L.; Wu, X.; Yang, W.; York, D. M.; Karplus, M. (2009)

CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and widely used molecular simulation program. It has been developed over the last three decades with a primary focus on molecules of biological interest, ...

Article

Chiral selectors in CE: Recent developments and applications (2012-mid 2014)

Stavrou, Ioannis J.; Mavroudi, Maria C.; Kapnissi‐Christodoulou, Constantina P. (2015)

There is a large number of chiral selectors (CSs) that have, over the years, been synthesized and used in electrophoretic enantioseparations. This report highlights the most important CSs applied in CE during the period ...

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

Computational protein design: The proteus software and selected applications

Simonson, T.; Gaillard, T.; Mignon, D.; Schmidt Am Busch, M.; Lopes, A.; Amara, Najette; Polydorides, Savvas; Sedano, A.; Druart, Karen; Archontis, Georgios Z. (2013)

We describe an automated procedure for protein design, implemented in a flexible software package, called Proteus. System setup and calculation of an energy matrix are done with the XPLOR modeling program and its sophisticated ...

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

Crossreactivity to vinculin and microbes provides a molecular basis for HLA-based protection against rheumatoid arthritis

Van Heemst, J.; Jansen, D. T. S. L.; Polydorides, Savvas; Moustakas, Antonis K.; Bax, M.; Feitsma, A. L.; Bontrop-Elferink, D. G.; Baarse, M.; Van Der Woude, D.; Wolbink, G. -J; Rispens, T.; Koning, F.; De Vries, R. R. P.; Papadopoulos, George K.; Archontis, Georgios Z.; Huizinga, T. W.; Toes, R. E. (2015)

The HLA locus is the strongest risk factor for anti-citrullinated protein antibody (ACPA) + rheumatoid arthritis (RA). Despite considerable efforts in the last 35 years, this association is poorly understood. Here we ...

Article

Design of a modified mouse protein with ligand binding properties of its human analog by molecular dynamics simulations: The case of C3 inhibition by compstatin

Tamamis, Phanourios; Pierou, P.; Mytidou, C.; Floudas, C. A.; Morikis, D.; Archontis, Georgios Z. (2011)

The peptide compstatin and its derivatives inhibit the complement-component protein C3 in primate mammals and are potential therapeutic agents against the unregulated activation of complement in humans, but are inactive ...

Article

Enthalpic Contribution to Protein Stability: Insights from Atom-Based Calculations and Statistical Mechanics

Lazaridis, T.; Archontis, Georgios Z.; Karplus, M. (1995)

This chapter discusses published analyses of protein stability based on model compound data and outlines the assumptions that have been made. The enthalpy of protein folding is considered and a thermodynamic cycle is used ...

Article

Glucose-based spiro-isoxazolines: A new family of potent glycogen phosphorylase inhibitors

Benltifa, Mahmoud; Hayes, Joseph M.; Vidal, Sébastien; Gueyrard, David; Goekjian, Peter G.; Praly, Jean Pierre; Kizilis, Gregory; Tiraidis, Costas; Alexacou, Kyra Melinda; Chrysina, Evangelia D.; Zographos, Spyros E.; Leonidas, Demetres D.; Archontis, Georgios Z.; Oikonomakos, Nikos G. (2009)

A series of glucopyranosylidene-spiro-isoxazolines was prepared through regio- and stereoselective [3+2]-cycloaddition between the methylene acetylated exo-glucal and aromatic nitrile oxides. The deprotected cycloadducts ...

Article

Implications of HIV-1 M group polymorphisms on integrase inhibitor efficacy and resistance: Genetic and structural in silico analyses

Loizidou, Eriketi Z.; Kousiappa, Ioanna; Zeinalipour-Yazdi, Constantinos D.; Van De Vijver, D. A. M. C.; Kostrikis, Leontios G. (2009)

The extensive polymorphisms among HIV-1 subtypes have been implicated in drug resistance development. Integrase inhibitors represent the latest addition to the treatment of HIV-1, and their efficacy and resistance patterns ...

Article

Implications of HIV-1 M group polymorphisms on integrase inhibitor efficacy and resistance: Genetic and structural in silico analyses

Loizidou, Eriketi Z.; Kousiappa, Ioanna; Zeinalipour-Yazdi, Constantinos D.; Van De Vijver, D. A. M. C.; Kostrikis, Leontios G. (2009)

The extensive polymorphisms among HIV-1 subtypes have been implicated in drug resistance development. Integrase inhibitors represent the latest addition to the treatment of HIV-1, and their efficacy and resistance patterns ...