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Selected Publications (Georgios Archontis)

 

1.        P. Tamamis, G. Archontis. (2011). Amyloid-like Self-Assembly of a Dodecapeptide Sequences from the Adenovirus Fiber Shaft: Perspectives from Molecular Dynamics Simulations. Journal of non-Crystalline Solids, 357 (2): 717-722. (Link)

2.        JM. Hayes, V. Skamnaki, G. Archontis, C. Lambrakis, J. Sarrou, N. Bischler, AL. Skaltsounis, SE Zographos, NG. Oikonomakos. (2011). Kinetics, in-silico docking, molecular dynamics and MM-GBSA binding studies on prototype indirubins, KT5720 and staurosporine as phosphorylase kinase ATP-binding site inhibitors: The role of water molecules. Proteins: Structure, Function and Bioinformatics, 79 (3): 703-719. (Link)

3.        P. Tamamis. D. Morikis, C. FLoudas and G. Archontis (2010). Species specificity of the complement inhibitor compstatin investigated by all-atom molecular dynamics simulations. Proteins: Structure, Function and Bioinformatics, 78 (12): 2655-2667. (Link)

4.        A. Aleksandrov S. Polydoridis, G. Archontis and T. Simonson (2010). Predicting the Acid/Base Behavior of Proteins: A constant-pH Monte Carlo Approach with Generalized Born Solvent. Journal of Physical Chemistry B, 114 (32): 10634-10648. (Link)

5.        P. Tamamis, E. Kasotakis, A. Mitraki and G. Archontis. (2009). Amyloid-like Self-Assembly of Peptide Sequences from the Adenovirus Fiber Shaft: Insights from Molecular Dynamics Simulations. Journal of Physical Chemistry B, 113 (47): 15639-15647. (Link)

6.        B.R.Brooks, C. L. Brooks III, A. D. Mackerell, L. Nilsson, R. J. Petrella, B. Roux, Y. Won, G. Archontis, C. Bartels, S. Boresch A. Caflisch, L. Caves, Q. Cui, A. R. Dinner, M. Feig, S. Fischer, J. Gao, M. Hodoscek, W. Im, K. Kuczera, T. Lazaridis, J. Ma, V. Ovchinnikov, E. Paci, R. W. Pastor, C. B. Post, J. Z. Pu, M. Schaefer, B. Tidor, R. M. Venable, H. L. Woodcock, X. Wu, W. Yang, D. M. York, and M. Karplus.(2009). CHARMM: The Biomolecular simulation Program. Journal of Computational Chemistry, 30: 1545-1615. (Link)

7.        P. Tamamis, L. Adler-Abramovich, M. Reches, K. Marshall, P. Sikorski, L. Serpell, E. Gazit and G. Achontis. (2009). Self-Assembly of Phenylalanine Oligopeptides: Insights from Experiments and Simulations. Biophysical Journal, 96: 5020-5029. (Link)

(SI)

8.        M. Benltifa, J.M. Hayes, S. Vidal, D. Gueyrard, P.G. Goekjian, J.-P. Praly, G. Kizilis, C. Tiraidis, K.-M. Alexacou, E.D. Chrysina, S.E. Zographos, D.D. Leonidas, G. Archontis and N.G. Oikonomakos (2009) Glucose-based spiro-isoxazolines: A new family of potent glycogen phosphorylase inhibitors. Bioorganic & Medicinal Chemistry, 17(20): 7368-7380. (Link)

9.        K.M. Alexacou, J.M. Hayes, C. Tiraidis, S.E. Zographos, D.D. Leonidas, E.D. Chrysina, G. Archontis, N.G. Oikonomakos, J.V. Paul, B. Varghese, and D. Loganathan (2008). Crystallographic and Computational studies on 4-phenyl-N-(β-D-glucopyranosyl)-1H-1,2,3-triazole-1-acetamide, an inhibitor of glycogen phosphorylase: comparison with a-D-glucose, N-acetyl-b-D-glucopyranosylamine and N-benzoyl-N/-b-D-glucopyranosyl urea binding. Proteins: Structure, Function and Bioinformatics,71(3): 1307-1323. (Link)

10.        P. Tamamis, S.S. Skourtis, D. Morikis, J.D. Lambris and G. Archontis. (2007). Conformational analysis of Compstatin analogues with Molecular Dynamics Simulations in Explicit Water. Journal of Molecular Graphics and Modelling, 26: 571-580(Link)

11.        S. Polydoridis, D. Leonidas, NG. Oikonomakos and G. Archontis (2007). Recognition of Ribonuclease A by 3'-5'-Pyrophosphate-linked Dinucleotide Inhibitors: a Molecular Dynamics/Continuum Electrostatics Analysis. Biophysical Journal, 92(5): 1659-1672. (Link)

12.        A. Lopes, A. Alexandrov, C. Bathelt, G. Archontis and T. Simonson (2007). Computational sidechain placement and protein mutagenesis with implicit solvent models. Proteins: Structure, Function and Bioinformatics,67(4): 853-867. (Link)

13.        G. Archontis and E. Leontidis (2006). Dissecting the stabilization of iodide at the air-water interface into components: A free energy analysis. Chemical Physics Letters 420:199-203. (Link)

14.     G. Archontis, E. Leontidis and G. Andreou (2005). Attraction of iodide ions by the free water surface, revealed by simulations with a polarizable force field, based on Drude oscillators. Journal of Physical Chemistry B, 109:17957-17966. (Link)

15.     G. Archontis and T. Simonson (2005). A residue-pairwise Generalized Born scheme, suitable for protein design simulations. Journal of Physical Chemistry B 109:22667-22673. (Link)

16.     G. Archontis, K.A. Watson, Q. Xie, G. Andreou, E. Chrysina, S.E. Zographos, N.G. Oikonomakos, L.N. Johnson and M. Karplus (2005). Molecular Recognition and Relative Binding of Glucopyranose Spirohydantoin Analogues to Glycogen Phosphorylase: A Free Energy Perturbation Study. Proteins, Structure Function and Bioinformatics 61:984-998. (Link)

17.     K.A. Watson, E.D. Chrysina, K.E. Tsitsanou, S.E. Zographos, D.D. Leonidas, G.W.J. Fleet, G. Archontis, and N.G. Oikonomakos, (2005). Kinetic and crystallographic studies of glucopyranose spirohydantoin and glucopyranosylamine analogues inhibitors of glycogen phosphorylaseProteins, Structure Function and Bioinformatics 61:966-983.

18.     G. Archontis and T. Simonson (2005). Proton binding to proteins: A self-consistent dielectric continuum analysis; Biophysical Journal 88:3888-3904. (Link)

19.     T. Simonson, G. Archontis and M. Karplus (2002). Protein-ligand recognition: Free-energy simulations come of age. Accounts of Chemical Research 35: 430-437. (Link)

20.     G. Archontis and T. Simonson (2001). Dielectric relaxation in an enzyme active site: Molecular dynamics simulations interpreted with a macroscopic continuum model.  Journal of the American Chemical Society 123: 11047-11056. (Link)

21.     G. Archontis, T. Simonson and M. Karplus (2001). Binding free energies and free energy components from molecular dynamics and Poisson Boltzmann calculations. Application to aminoacid recognition by Aspartyl-tRNA synthetase. Journal of Molecular Biology 306: 307-327. (Link)