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Georgios Archontis - Publications

Affiliations: 
1996- Physics University of Cyprus, Nicosia, Nicosia, Cyprus 
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47 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2022 Michael E, Polydorides S, Archontis G. Computational Design of Peptides with Improved Recognition of the Focal Adhesion Kinase FAT Domain. Methods in Molecular Biology (Clifton, N.J.). 2405: 383-402. PMID 35298823 DOI: 10.1007/978-1-0716-1855-4_18  0.377
2020 Michael E, Polydorides S, Promponas VJ, Skourides P, Archontis G. Recognition of LD motifs by the focal adhesion targeting domains of focal adhesion kinase and proline-rich tyrosine kinase 2-beta: Insights from molecular dynamics simulations. Proteins. PMID 32776636 DOI: 10.1002/Prot.25992  0.389
2020 Michael E, Polydorides S, Simonson T, Archontis G. Hybrid MC/MD for protein design. The Journal of Chemical Physics. 153: 054113. PMID 32770896 DOI: 10.1063/5.0013320  0.388
2019 Sullivan MV, Dennison SR, Archontis G, Reddy SM, Hayes JM. Towards Rational Design of Selective Molecularly Imprinted Polymers (MIPs) for Proteins: Computational and Experimental Studies of Acrylamide-Based Polymers for Myoglobin. The Journal of Physical Chemistry. B. PMID 31150581 DOI: 10.1021/Acs.Jpcb.9B03091  0.375
2017 Michael E, Polydorides S, Simonson T, Archontis G. Simple models for nonpolar solvation: Parameterization and testing. Journal of Computational Chemistry. 38: 2509-2519. PMID 28786118 DOI: 10.1002/Jcc.24910  0.414
2016 Polydorides S, Michael E, Mignon D, Druart K, Archontis G, Simonson T. Proteus and the Design of Ligand Binding Sites. Methods in Molecular Biology (Clifton, N.J.). 1414: 77-97. PMID 27094287 DOI: 10.1007/978-1-4939-3569-7_6  0.426
2015 Gorham RD, Forest DL, Khoury GA, Smadbeck J, Beecher CN, Healy ED, Tamamis P, Archontis G, Larive CK, Floudas CA, Radeke MJ, Johnson LV, Morikis D. New compstatin peptides containing N-terminal extensions and non-natural amino acids exhibit potent complement inhibition and improved solubility characteristics. Journal of Medicinal Chemistry. 58: 814-26. PMID 25494040 DOI: 10.1021/Jm501345Y  0.731
2014 Tamamis P, Kasotakis E, Archontis G, Mitraki A. Combination of theoretical and experimental approaches for the design and study of fibril-forming peptides. Methods in Molecular Biology (Clifton, N.J.). 1216: 53-70. PMID 25213410 DOI: 10.1007/978-1-4939-1486-9_3  0.698
2014 Tamamis P, Kieslich CA, Nikiforovich GV, Woodruff TM, Morikis D, Archontis G. Insights into the mechanism of C5aR inhibition by PMX53 via implicit solvent molecular dynamics simulations and docking. Bmc Biophysics. 7: 5. PMID 25170421 DOI: 10.1186/2046-1682-7-5  0.706
2014 Tamamis P, Terzaki K, Kassinopoulos M, Mastrogiannis L, Mossou E, Forsyth VT, Mitchell EP, Mitraki A, Archontis G. Self-assembly of an aspartate-rich sequence from the adenovirus fiber shaft: insights from molecular dynamics simulations and experiments. The Journal of Physical Chemistry. B. 118: 1765-74. PMID 24437637 DOI: 10.1021/Jp409988N  0.697
2013 Simonson T, Gaillard T, Mignon D, Schmidt am Busch M, Lopes A, Amara N, Polydorides S, Sedano A, Druart K, Archontis G. Computational protein design: the Proteus software and selected applications. Journal of Computational Chemistry. 34: 2472-84. PMID 24037756 DOI: 10.1002/Jcc.23418  0.431
2013 Gorham RD, Forest DL, Tamamis P, López de Victoria A, Kraszni M, Kieslich CA, Banna CD, Bellows-Peterson ML, Larive CK, Floudas CA, Archontis G, Johnson LV, Morikis D. Novel compstatin family peptides inhibit complement activation by drusen-like deposits in human retinal pigmented epithelial cell cultures. Experimental Eye Research. 116: 96-108. PMID 23954241 DOI: 10.1016/J.Exer.2013.07.023  0.738
2013 Ioannou F, Leontidis E, Archontis G. Helix formation by alanine-based peptides in pure water and electrolyte solutions: insights from molecular dynamics simulations. The Journal of Physical Chemistry. B. 117: 9866-76. PMID 23919617 DOI: 10.1021/Jp406231G  0.45
2012 Tamamis P, López de Victoria A, Gorham RD, Bellows-Peterson ML, Pierou P, Floudas CA, Morikis D, Archontis G. Molecular dynamics in drug design: new generations of compstatin analogs. Chemical Biology & Drug Design. 79: 703-18. PMID 22233517 DOI: 10.1111/J.1747-0285.2012.01324.X  0.743
2012 A. Kieslich C, Tamamis P, D. Gorham Jr. R, Lopez de Victoria A, U. Sausman N, Archontis G, Morikis D. Exploring Protein-Protein and Protein-Ligand Interactions in the Immune System using Molecular Dynamics and Continuum Electrostatics Current Physical Chemistry. 2: 324-343. DOI: 10.2174/1877946811202040324  0.66
2012 de Victoria AL, Tamamis P, Gorham RD, Kieslich CA, Bellows-Peterson ML, Floudas CA, Archontis G, Morikis D. Computational and Experimental Analysis of the Interactions Between C3 and Compstatin Family Peptides Biophysical Journal. 102: 62a. DOI: 10.1016/J.Bpj.2011.11.371  0.753
2011 Tamamis P, Pierou P, Mytidou C, Floudas CA, Morikis D, Archontis G. 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. Proteins. 79: 3166-79. PMID 21989937 DOI: 10.1002/Prot.23149  0.736
2011 Ioannou F, Archontis G, Leontidis E. Specific interactions of sodium salts with alanine dipeptide and tetrapeptide in water: insights from molecular dynamics. The Journal of Physical Chemistry. B. 115: 13389-400. PMID 21978277 DOI: 10.1021/Jp207068M  0.441
2011 Polydorides S, Amara N, Aubard C, Plateau P, Simonson T, Archontis G. Computational protein design with a generalized Born solvent model: application to Asparaginyl-tRNA synthetase. Proteins. 79: 3448-68. PMID 21563215 DOI: 10.1002/Prot.23042  0.473
2011 Pieridou G, Avgousti-Menelaou C, Tamamis P, Archontis G, Hayes SC. UV resonance Raman study of TTR(105-115) structural evolution as a function of temperature. The Journal of Physical Chemistry. B. 115: 4088-98. PMID 21428385 DOI: 10.1021/Jp107519B  0.67
2011 Hayes JM, Skamnaki VT, Archontis G, Lamprakis C, Sarrou J, Bischler N, Skaltsounis AL, Zographos SE, Oikonomakos NG. 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 examined. Proteins. 79: 703-19. PMID 21287607 DOI: 10.1002/Prot.22890  0.367
2011 Pieridou G, Avgousti-Menelaou C, Tamamis P, Archontis G, Hayes SC. Correction to “UV Resonance Raman Study of TTR(105–115) Structural Evolution as a Function of Temperature” The Journal of Physical Chemistry B. 115: 9337-9337. DOI: 10.1021/Jp205360X  0.599
2011 Tamamis P, Archontis G. Amyloid-like self-assembly of a dodecapeptide sequence from the adenovirus fiber shaft: Perspectives from molecular dynamics simulations Journal of Non-Crystalline Solids. 357: 717-722. DOI: 10.1016/J.Jnoncrysol.2010.05.083  0.693
2010 Aleksandrov A, Polydorides S, Archontis G, Simonson T. Predicting the acid/base behavior of proteins: a constant-pH Monte Carlo approach with generalized born solvent. The Journal of Physical Chemistry. B. 114: 10634-48. PMID 20701391 DOI: 10.1021/Jp104406X  0.372
2010 Tamamis P, Morikis D, Floudas CA, Archontis G. Species specificity of the complement inhibitor compstatin investigated by all-atom molecular dynamics simulations. Proteins. 78: 2655-67. PMID 20589629 DOI: 10.1002/Prot.22780  0.732
2010 Simonson T, Archontis G, Karplus M. ChemInform Abstract: Free Energy Simulations Come of Age: Protein-Ligand Recognition Cheminform. 33: no-no. DOI: 10.1002/chin.200237290  0.437
2009 Tamamis P, Kasotakis E, Mitraki A, Archontis G. Amyloid-like self-assembly of peptide sequences from the adenovirus fiber shaft: insights from molecular dynamics simulations. The Journal of Physical Chemistry. B. 113: 15639-47. PMID 19863125 DOI: 10.1021/Jp9066718  0.716
2009 Benltifa M, Hayes JM, Vidal S, Gueyrard D, Goekjian PG, Praly JP, Kizilis G, Tiraidis C, Alexacou KM, Chrysina ED, Zographos SE, Leonidas DD, Archontis G, Oikonomakos NG. Glucose-based spiro-isoxazolines: a new family of potent glycogen phosphorylase inhibitors. Bioorganic & Medicinal Chemistry. 17: 7368-80. PMID 19781947 DOI: 10.1016/J.Bmc.2009.08.060  0.342
2009 Tamamis P, Adler-Abramovich L, Reches M, Marshall K, Sikorski P, Serpell L, Gazit E, Archontis G. Self-assembly of phenylalanine oligopeptides: insights from experiments and simulations. Biophysical Journal. 96: 5020-9. PMID 19527662 DOI: 10.1016/J.Bpj.2009.03.026  0.7
2009 Brooks BR, Brooks CL, Mackerell AD, Nilsson L, Petrella RJ, Roux B, Won Y, Archontis G, Bartels C, Boresch S, Caflisch A, Caves L, Cui Q, Dinner AR, Feig M, et al. CHARMM: the biomolecular simulation program. Journal of Computational Chemistry. 30: 1545-614. PMID 19444816 DOI: 10.1002/Jcc.21287  0.666
2008 Alexacou KM, Hayes JM, Tiraidis C, Zographos SE, Leonidas DD, Chrysina ED, Archontis G, Oikonomakos NG, Paul JV, Varghese B, Loganathan D. Crystallographic and computational studies on 4-phenyl-N-(beta-D-glucopyranosyl)-1H-1,2,3-triazole-1-acetamide, an inhibitor of glycogen phosphorylase: comparison with alpha-D-glucose, N-acetyl-beta-D-glucopyranosylamine and N-benzoyl-N'-beta-D-glucopyranosyl urea binding. Proteins. 71: 1307-23. PMID 18041758 DOI: 10.1002/Prot.21837  0.352
2007 Tamamis P, Skourtis SS, Morikis D, Lambris JD, Archontis G. Conformational analysis of compstatin analogues with molecular dynamics simulations in explicit water. Journal of Molecular Graphics & Modelling. 26: 571-80. PMID 17498990 DOI: 10.1016/J.Jmgm.2007.03.014  0.694
2007 Lopes A, Alexandrov A, Bathelt C, Archontis G, Simonson T. Computational sidechain placement and protein mutagenesis with implicit solvent models. Proteins. 67: 853-67. PMID 17348031 DOI: 10.1002/Prot.21379  0.351
2007 Polydoridis S, Leonidas DD, Oikonomakos NG, Archontis G. Recognition of ribonuclease A by 3'-5'-pyrophosphate-linked dinucleotide inhibitors: a molecular dynamics/continuum electrostatics analysis. Biophysical Journal. 92: 1659-72. PMID 17142283 DOI: 10.1529/Biophysj.106.093419  0.391
2006 Archontis G, Leontidis E. Dissecting the stabilization of iodide at the air–water interface into components: A free energy analysis Chemical Physics Letters. 420: 199-203. DOI: 10.1016/J.Cplett.2005.12.051  0.341
2005 Archontis G, Simonson T. A residue-pairwise generalized born scheme suitable for protein design calculations. The Journal of Physical Chemistry. B. 109: 22667-73. PMID 16853951 DOI: 10.1021/Jp055282+  0.388
2005 Archontis G, Watson KA, Xie Q, Andreou G, Chrysina ED, Zographos SE, Oikonomakos NG, Karplus M. Glycogen phosphorylase inhibitors: a free energy perturbation analysis of glucopyranose spirohydantoin analogues. Proteins. 61: 984-98. PMID 16245298 DOI: 10.1002/Prot.20641  0.523
2005 Watson KA, Chrysina ED, Tsitsanou KE, Zographos SE, Archontis G, Fleet GW, Oikonomakos NG. Kinetic and crystallographic studies of glucopyranose spirohydantoin and glucopyranosylamine analogs inhibitors of glycogen phosphorylase. Proteins. 61: 966-83. PMID 16222658 DOI: 10.1002/Prot.20653  0.324
2005 Archontis G, Simonson T. Proton binding to proteins: a free-energy component analysis using a dielectric continuum model. Biophysical Journal. 88: 3888-904. PMID 15821163 DOI: 10.1529/Biophysj.104.055996  0.44
2002 Simonson T, Archontis G, Karplus M. Free energy simulations come of age: protein-ligand recognition. Accounts of Chemical Research. 35: 430-7. PMID 12069628 DOI: 10.1021/Ar010030M  0.562
2001 Archontis G, Simonson T, Karplus M. Binding free energies and free energy components from molecular dynamics and Poisson-Boltzmann calculations. Application to amino acid recognition by aspartyl-tRNA synthetase. Journal of Molecular Biology. 306: 307-27. PMID 11237602 DOI: 10.1006/Jmbi.2000.4285  0.55
1999 Simonson T, Archontis G, Karplus M. A Poisson−Boltzmann Study of Charge Insertion in an Enzyme Active Site:  The Effect of Dielectric Relaxation The Journal of Physical Chemistry B. 103: 6142-6156. DOI: 10.1021/Jp991354J  0.444
1998 Archontis G, Simonson T, Moras D, Karplus M. Specific amino acid recognition by aspartyl-tRNA synthetase studied by free energy simulations. Journal of Molecular Biology. 275: 823-46. PMID 9480772 DOI: 10.1006/Jmbi.1997.1470  0.561
1997 Simonson T, Archontis G, Karplus M. Continuum Treatment of Long-Range Interactions in Free Energy Calculations. Application to Protein−Ligand Binding. The Journal of Physical Chemistry B. 101: 8349-8362. DOI: 10.1021/Jp9711499  0.485
1996 Lazaridis T, Archontis G, Karplus M. Enthalpic contribution to protein stability: insights from atom-based calculations and statistical mechanics. Advances in Protein Chemistry. 47: 231-306. PMID 8561050 DOI: 10.1016/S0065-3233(08)60547-1  0.68
1996 Archontis G, Karplus M. Cumulant expansion of the free energy: Application to free energy derivatives and component analysis The Journal of Chemical Physics. 105: 11246-11260. DOI: 10.1063/1.472921  0.459
1994 Boresch S, Archontis G, Karplus M. Free energy simulations: the meaning of the individual contributions from a component analysis. Proteins. 20: 25-33. PMID 7824520 DOI: 10.1002/Prot.340200105  0.712
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