Georgios Archontis

Last Updated: 9/2013

 

Current position:

 Associate Professor, Department of Physics, University of Cyprus. Email: archonti@ucy.ac.cy; webpage: www.biophys.ucy.ac.cy; Tel: +357 22 89 28 22; Fax: +357 22 89 28 21.

 

Employment History:

Š      University of Cyprus, Associate Professor, Department of Physics, 7/2007 – today.

Š      University of Cyprus, Assistant. Professor, Department of Physics, 10/2002 – 7/2007.

Š      University of Cyprus, Lecturer, Department of Physics, 1/2001 – 10/2002. University of Cyprus, Lecturer, Department of Natural Sciences, 10/1996 – 1/2001.

Š      Ecole Polytechnique, Paris, France. Visiting Professor (Sabbatical leave), 1/2005 – 11/2005.

Š      University Louis Pasteur, Strasbourg, France. Post-Doctoral Associate, Laboratoire de Chimie Biophysique, 6/1994 – 8/1996.

Š      Harvard University, USA. Research Assistant, Committee on Higher Degrees in Biophysics, August 1988 – June 1994.

Š      Harvard University, USA. Teaching Assistant, Committee on Higher Degrees in Biophysics, 1990-1993.

 

Education:

Š      Harvard University, USA. Ph.D, Committee on Higher Degrees in Biophysics (1994). Dissertation title: Statistical Mechanical Studies of Proteins”. Research supervisor: Martin Karplus.

Š      University of Athens, Greece. B.S. in Physics (1987); GPA 9.41/10 (highest GPA of the graduating year; 300 students).

 

Stipends:

Š      Human Capital and Mobility:Research Fellow (1995-1996).

Š      Harvard University: Research Fellow (1988-1994).

Š      Harvard University: Teaching Fellow. Statistical Thermodynamics” (1990-1991), 3rd-year undergraduate course.

Š      Harvard University: Teaching Fellow. Statistical Mechanics”, graduate course for Physics and Chemistry students, (1991-1992).

Š      Harvard University: Teaching Fellow. Statistical Mechanics”, graduate course for Physics and Chemistry students, (1992-1993).

Š      Greek Science Foundation (IKY: (1983-1987). Yearly awards for highest undergraduate grade point average (9.41/10) in the Dept. of Physics, University of Athens.

Š      Papadakis Foundation. Fellowship for excellence in undergraduate studies (1985-1987).

 

Brief Description of Research

 

My research aims to understand the properties of biomolecular systems by means of computational methodologies (molecular dynamics simulations with atomic-detail or implicit-solvent models) and theoretical concepts, (based on statistical mechanics, continuum electrostatics). I am among the developers of the widely used biomolecular program Chemistry at Harvard Molecular Mechanics (CHARMM).

 

My research activity during my employment at the University of Cyprus (August 1996 – today) can be grouped in the following areas; relevant publications are included in braces, following the numbering in my publication-list.

 

1.     Self-assembly properties of peptide-based nanostructures [1, 8, 11, 15, 17].

2.     Molecular interactions that confer stability and specificity in several biomolecular complexes [4-6, 9, 12, 14, 18-19, 21, 26-27, 29-30, 32, 36-37, 39, 41].

3.     Development and use of accurate and efficient approximations to many-body free-energy functions, that model solvent-protein interactions and can be used in high-throughput protein- and ligand design calculations [2, 10, 13, 22, 24].

4.     Structural and thermodynamical properties of electrolyte solutions by simulations with biomolecular Hamiltonians with or without explicit polarisability [3, 7, 23, 25].

5.     Proton-binding phenomena and protein dielectric relaxation [13, 28, 35].

 

International Collaborations:

 

Š      Prof. Martin Karplus, Department of Chemistry and Chemical Biology, Harvard University, USA, and Laboratoire de Chimie Biophysique, University Louis Pasteur, Strasbourg, France.

Š      Prof. Christodoulos A. Floudas, Department of Chemical Engineering, Princeton University, USA.

Š      Prof. Thomas Simonson, Laboratoire de Biochimie, Département de Biologie, Ecole Polytechnique, France.

Š      Prof. Dimitrios Morikis, Department of Bioengineering, University of California Riverside, USA.

Š      Prof. Ehud Gazit, Department of Molecular Biology and Biotechnology, Tel Aviv University, Israel.

Š      Prof. Anna Mitraki (Department of Materials Science and Technology, University of Crete, Greece.

Š      Dr. Joe Hayes, National Hellenic Research Foundation, Athens,  Greece.

 

Local Collaborations:

Š      Prof. Epameinondas Leontidis, Department of Chemistry.

Š      Prof. Sophia Hayes, Department of Chemistry.

Š      Prof. Spiros Skourtis, Department of Physics.

 

Awarded Research Programs:

The following Research Grants were awarded on a competitive basis, after evaluation of international expert referees (Coordinator in programs 1-3, 5-14):

1.     Regulation of the Complement C5aR Receptor: Insights from Molecular Dynamics Simulations”. Grant from the University of Cyprus, (2013-2015, 80,000 Euro); Coordinator.

2.     Self-Assembly and Folding of biologically-inspired Peptide Sequences From Natural Fibrous Proteins: Insights From Highly-Intensive Computational Studies”. Grant for the Upgrade of Existing Infrastructure”, provided by the Cyprus Research Promotion Foundation (RPF), (2012-2015, 100,000 Euro); Coordinator.

3.     Computational Investigation of Peptide Sequences from the Adenovirus and Reovirus Fiber Shaft: Insights on the Self-assembly of Peptide-based Nanostructures and the Stability of the Triple-β Spiral Fold”. Grant provided by the University of Cyprus (2011-2012, 85,000 Euro); Coordinator.

4.     CyTera: A multi-Teraflop computing Facility For Science and Technology in Cyprus”. Grant for Strategic Infrastructure, provided by the Cyprus RPF (2009-2013, 1.7 million Euro). International consortium of the University of Cyprus, the National Center for Supercomputing Applications (NCSA), USA, the Juelich Supercomputing center and the Synchrotron-light for Experimental Science and Applications in the Middle East; Participant.

5.     Computational Study of ionic effects on the conformational stability and the helix/coil equilibrium of model oligopeptides”. PENEK” grant for the support of a graduate student (PhD), provided by the Cyprus RPF (2008-2011, 90,000 Euro); Coordinator.

6.     Protein design simulations and application in the genetic engineering of synthetases”, Grant for the Promotion of the Cyprus – France Technology and Scientific Cooperation, provided by the Cyprus RPF (2008-2010, 7,000 Euro); Coordinator.

7.     Computational investigation of the salting-out effect with polarizable water models”. Grant provided by the A.G. Leventis Foundation (2006-2009, 110,000 Euro); Coordinator.

8.     Modification of the specificity of aminoacyl-tRNA syntethases by biomolecular simulations”. PENEK” grant for the support of a graduate student (PhD), provided by the Cyprus RPF (2006-2009, 77,000 Euro); Coordinator.

9.     Study of the solvation of organic compounds in electrolyte solutions by molecular dynamics simulations”. PENEK” grant for the support of a graduate (Masters) student, provided by the Cyprus RPF (2006-2007, 27,000 Euro); Coordinator.

10.  Redesigning the genetic code with biomolecular simulation methods”. Grant for the Promotion of the Cyprus – France Technology and Scientific Cooperation”, provided by the Cyprus RPF (2004-2006, 7,000 Euro); Coordinator.

11.  Study of Compstatin, inhibitor of the autoimmune system, with high-accuracy molecular simulations”. Grant for the Development of Existing Infrastructure”, provided by the Cyprus RPF (2004-2007, 48,000 Euro); Research Coordinator.

12.  Study of the initial formation of amyloid fibers from peptides that influence the formation of type-II diabetes. Microscopic understanding with atomic-detail simulations”. PENEK” grant for the support of a graduate (Masters) student, provided by the Cyprus RPF (2004-2005, 16,000 Euro); Coordinator.

13.  Regulation of Glycogen metabolism and oxidative repair of DNA by molecular association; Insights from simulations and experiment ”. Research grant provided by the A.G. Leventis Foundation (2002-2004, 35,000 Euro); Coordinator (with Prof. Spiros Skourtis).

14.  Molecular Recognition and Rational Drug Design of new Drugs”. Grant for the Promotion of the Cyprus – France Technology and Scientific Cooperation”, provided by the Cyprus RPF (2001-2003, 13,000 Euro); Coordinator.

15.  From Strong Interactions to Molecular Recognition: Theoretical and Computational studies”. University of Cyprus (1996-2000, 100,000 Euro); Participant (with S. Skourtis, H. Panagopoulos, C. Alexandrou).

 

 

Supervision of Post-doctoral Research Assistants:

 

1.     Dr. Savvas Polydoridis (9/2013 - ). Research Funded under research program 1.

2.     Dr. Phanourios Tamamis (6/2010-12/2012). Research funded under research programs Nr 1, 2 and 3 (above).

3.     Dr. Cosmina Dutan (10/2006-9/2009). Research funded under research program Nr. 7.

4.     Dr. Majid Monajjemi (February-September 2003). Funded by research program Nr. 13.

5.     Dr. Qian Xie (1997-2000). Funded by research program Nr. 15.

 

 

Supervision of graduate (PhD) Students:

 

1.     Elena Michael (9/2013-). Regulation of the Complement C5aR Receptor: Insights from Molecular Dynamics Simulations”. Supported by research program Nr. 1

2.     Philippos Ioannou (9/2008-1/2013) Computational Study of Ionic Effects on the Conformational Stability and the Helix/Coil Equilibrium of Model Oligopeptides”; supported by research program Nr. 5.

3.     Phanourios Tamamis (9/2006-5/2010). Molecular Dynamics studies of the structural, dynamical and thermodynamical properties of biomolecular complexes in explicit and implicit solvent models”; partially funded by research program Nr. 7.

4.     Savvas Polydoridis (9/2006-5/2011). Redesigning the specificity of Aminoacyl-tRNA Synthetases with Biomolecular Simulations”; supported by research program Nr. 8.

 

Supervision of graduate (Masters) Theses:

 

1.     Chrystalla Mytidou (2010-2012). Study of the Structural Stability of Protein Segments from the Adenovirus Fiber and of Biomolecular Complexes Implicated in the Function of the Complement System; Insights from Molecular Dynamics simulations”.

2.     Philippos Ioannou (2006-2008). Investigation of the air/water interface of alcohol-water mixtures by MD simulations”; supported by research program Nr. 9.

3.     Georgios Spyrou (2004-2006). Investigation of the formation of amyloid fibers by peptidic analogues of silk-worm chorion proteins, with folding simulations”.  

4.     Savvas Polydoridis (2003-2005). Application of Free Energy Calculations to the Thermodynamic stability of Biomolecular Complexes”; supported by research program Nr. 12.

5.     Georgia Andreou (2002-2005) Simulations of hydrated ions with polarized ion- and water models” (GA did her Masters studies in the Dept. of Chemistry. U. of  Cyprus; she was co-advised by Prof. E. Leontidis).

 

Supervision of Undergraduate Theses:

 

1.     Michalis Kassinopoulos (2012-2013). Molecular Dynamics Simulations of a peptide from the adenovirus fiber shaft, with the potential to self-assemble in amyloid-like nanostructures”.

2.     Zena Scotti (2010-2011). Self-assembly of a peptide sequence from the adenovirus fiber shaft: Insights from Molecular Dynamics simulations with implicit and explicit solvent representations”.

3.     Elena Demosthenous (2010-2011). Structural and dynamical properties of peptidic sequences”.

4.     Panagiota Pierrou (2010-2011). Computer-aided design of compstatin-based inhibitors of the autoimmune complement component protein C3”.

5.     Andreas Kalli (2007-2008). Self-assembly of a peptidic analogue from the silkmoth chorion protein.

6.     Phanourios Tamamis (2005-2006). Analysis of the structural and dynamical properties of compstatin in solution, by explicit water molecular dynamics simulations”, 1st prize in the Competition for Undergraduate Students Research in Cyprus (PROFOIT), Cyprus RPF.

7.     Savvas Polydoridis (2002-2003). The protein folding problem; theory and simulations”.

8.     Georgia Andreou (2001-2002). Conformational stability of biomolecular systems in solution, studied by explicit and implicit solvent models”.

 

Teaching Experience

 

 

University of Cyprus (1996 - )

 

During my academic career at the University of Cyprus, I have been solely responsible for the teaching of the following courses:

 

A)   Undergraduate Courses:

 

1.     Physics for the Medical School (2012-). This course presents a wide collection of physics areas (mechanics, fluid mechanics, elasticity theory, waves, electrostatics, nuclear physics, molecular biophysics) to 1st-year medical students. A large emphasis is given on the application of physics principles to the human body.

2.     General Physics II: Principles of Electricity and Electromagnetism (2012-). Introductory core course, 1st year undergraduate students in Physics.

3.     Biophysics (2010-). Elective course, 4th year undergraduate students in Physics.

4.     Physics for Chemists (2007-2011). Core course, 1st year undergraduate students in Chemistry.

5.     Computational Physics (2003-2010). Elective course, for 3rd-4th year undergraduate students in Physics.

6.     Thermodynamics and Statistical Mechanics (1996-2005, 2009, 2011). Core course, 3rd year undergraduate students in Physics.

7.     Computer Applications in the Physical Sciences (1999-2000). Core course, 1st year undergraduate students in Physics.

8.     Principles of Physics for non-Physics majors (1996-2000). Undergraduate students with non-Physics concentration.

9.     Mathematical Methods in the Physical Sciences (1996-1998). 1st year undergraduate students in Physics and Chemistry.

 

B)   Graduate Courses:

 

1.     Graduate Statistical Mechanics (2004-). Core course, 1st year graduate students in Physics (Masters in mainstream Physics, PhD).

2.     Graduate Statistical and Computational Physics of Biomolecular Systems (2004-). Specialized course for graduate students in Biophysics (Masters in mainstream Physics, PhD).

 

 

University of Athens

 

1.     Computational Analysis of Biomolecular Structures (2004-) Series of lectures and computational applications for students in the graduate program Masters in Bioinformatics”, University of Athens.

 

Harvard University

 

During my graduate studies, I worked as teaching assistant in the following courses:

 

1.     Statistical Thermodynamics (1990-1991). 3rd year undergraduate course in the Dept. of Chemistry.

2.     Statistical Mechanics (1992-1993 & 1993-1994). Graduate-level course taken by students from the Departments of Chemistry and Physics.

 

 

Membership in Editorial Boards:

 

Š      Associate Editor, BMC Biophysics; Published by BioMed Central;

http://www.biomedcentral.com/bmcbiophys/edboard/

Š      Εditor, Computational and Mathematical methods in Medicine. Hindawi; http://www.hindawi.com/journals/cmmm/editors/

 

 

Administration Duties:

 

Š      Chairman, Department of Physics, University of Cyprus (3/2012-today).

Š      Vice-Chairman, Department of Physics, University of Cyprus (3/2010-3/2012).

Š      Coordinator of the Undergraduate Student Program in the Department of Physics, University of Cyprus (2006-2012).

Š      Coordinator of the Department of Physics (faculty and student) exchanges under the program ERASMUS (2000-2005).

Š      Member of the Cyprus Academic Committee for the SESAME program (up to 2000). Co-organized the 2nd Workshop on Structural Molecular Biology at SESAME (Nicosia, 6-7 December 2000)

Details are in http://www.sesame.org.jo/publication/SRNewsDec62000.aspx

 

 

Other Duties:

 

Š      Regular reviewer for the journals Biophysical Journal, Journal of Physical Chemistry B, Journal of Chemical Theory and Computation, Journal of the American Chemical Society, Proteins: Structure, Function and Bioinformatics, Journal of Non-crystalline solids, Soft Matter, Bioorganic and Medicinal Chemistry.

Š      Member of the Biophysical Society.

 

Conference Organization:

 

Š      Dynamics and Thermodynamics of Biomolecular Recognition”. CECAM workshop, 5-7/5/2011, Ecole Polytechnique, Paris. Co-organizers: Prof. Thomas Simonson, Ecole Polytechnique, France; Prof. Jonathan Essex, University of Southampton, UK.

Details are in http://www.cecam.org/workshop-596.html.

Š      2nd Workshop on Structural Molecular Biology at SESAME (Nicosia, 6-7/12/2000). Details are in http://www.sesame.org.jo/publication/SRNewsDec62000.aspx

 

Talks in International Conferences (2000-2013)

 

1.     Regulation of Proteins Implicated in the Function of the Complement System: Insights from MD Simulations. CHARMM Developers Meeting, Zurich, June 25-28, 2013.

2.     Compstatin and Human C3 interactions. Theoretical Approaches for the Genome and Proteins (TAGp 2012). LAPTh, Annecy-Le-Vieux, December 3-4, 2012.

3.     Development of Regulatory Compounds for the Complement System by MD simulations and Experiments. From Computational Biophysics to Systems Biology 2012 (CBSB12), Knoxville, Tennessee, June 3-5, 2012; Talk given by P. Tamamis (CBSB12 Outstanding Young Researcher Talk).

4.     Automated Design of Protein-Ligand Interactions with a Generalized Born Solvent Model.  CECAM Meeting on Dynamics and Thermodynamics of Biomolecular Recognition”, 2011 (coorganizer). Ecole Polytechnique, Paris, May 5-7, 2011.

5.     Molecular Dynamics Simulations Tackle the Species Specificity of the Complement Inhibitor Compstatin by Designing Transgenic Animal Proteins and De Novo Dual-Specificity Ligands; Talk by P. Tamamis, International Conference on Statistical Physics, 2011. Larnaca, Cyprus, July 11-15, 2011.

6.     Molecular Dynamics in Drug Design; Talk by P. Tamamis, Hellenic Chemical Society Meeting, 2011. October 2011, Limassol, Cyprus.

7.     Self-assembly of short peptide sequences from a natural fibrous protein, the Adenovirus fiber shaft. Workshop on Coarse-graining of many-body systems: analysis, computations and applications, University of Crete, June 2011. Heraklion, Greece, 2011 (talk by P. Tamamis).

8.     MD-based Drug Design of the Complement Inhibitor Compstatin. Navigating Chemical Compound Space for Materials and Bio-Design. Workshop I: Design of Drugs and Chemicals that Influence Biology. University of California at Los Angeles, 2011. UCLA, U.S.A. April 2011 (talk by P. Tamamis).

9.     Inhibition of C3 by Compstatin analogs: Insights from Molecular dynamics Simulations. Theoretical Approaches for the Genome and the Proteins (TAGp), Laboratoire de Physique Theorique, Annecy-le-Vieux, University of Savoie, October 20-22, 2010.

10.  Inhibition of C3 by Compstatin analogs: Insights from Molecular dynamics Simulations. CHARMM developers meeting, July 25-27, 2010, Harvard University.

11.  Insights on the Self-Assembly of Oligopeptides by Implicit-Solvent Simulations. CHARMM developers meeting, June 26-27, 2009, Stockholm, Sweden.

12.  Oligopeptide self-assembly: Insights from Experiments and Simulations. Nanotheranostics: International Conference on Fabrication and Safety, 2010. Ayia Napa, Cyprus, May 2010.

13.  Oligopeptide Nanostructure Formation: Insights from Experiments and Implicit-Solvent Simulations. 6th International Discussion Meeting on relaxations in Complex Systems: Special session Frontiers in Biophysics”. August 30- September 5 2009, Universita di Roma la Sapienza.

14.  Self-Assembly of Phenylalanine Oligopeptides: Insights from experimental and computational studies; Presented by P. Tamamis, European Biophysics Congress 2009, July 11-15 2009, Genoa, Italy.

15.  Self-Assembly of Phenylalanine Oligopeptides and Peptide Sequences from the Adenovirus Fiber Shaft. Biomolecular Modeling and Simulations 2009”, Weizmann Institute and Israel Science Foundation; Presented by P. Tamamis, September 13-16 2009, Safed, Israel.

16.  Computational and experimental insights into the self-assembly of diphenylalanine and triphenylalanine peptides. 4th Conference of the Hellenic Society for Computational Biology, HSCBB09”, National Hellenic Research Foundation; Presented by P. Tamamis, December 18-20 2009, Athens, Greece.

17.  From Adenovirus Peptidic Sequences Self-assembly to Nanocircuitry: Can MD Simulations Bridge the Gap? 4th Conference of the Hellenic Society for Computational Biology, HSCBB09”, National Hellenic Research Foundation; Presented by P. Tamamis, December 18-20 2009, Athens, Greece.

18.  Thermodynamic Stability of Protein-Ligand Complexes: Insights from free-energy simulations. Approaches to Computational Biophysics. December 5-6, 2008, National Hellenic Research Foundation, Athens.

19.  Insights on Biomolecular Association from implicit-solvent simulations. Approaches to Computational Biophysics. December 5-6, 2008, National Hellenic Research Foundation, Athens.

20.  Insights into the Self-assembly of Phenylalanine Oligopeptides by Replica Exchange MD Simulations with the GBSW Implicit-Solvent Model. From Computational Biophysics to Systems Biology 2008; Presented by P. Tamamis, Juelich, Germany, May 19-21, 2008.

21.  Conformational Investigation of an Octapeptide Amyloidogenic Sequence from the Adenovirus Fiber Shaft by Replica-Exchange Simulations in Implicit Solvent. SIMBIOMA2008, Molecular Simulations in Biosystems and Material Science (European Science Foundation; Presented by P. Tamamis, Konstanz, Germany, April 02-05, 2008.

22.  A Continuum Electrostatics Model for Free Energy Changes due to Charge Perturbations: Application to proton binding. CHARMM developers meeting, July 20-22 2007, Harvard University, USA.

23.  Insights on the Structural, Dynamical and Thermodynamical Properties of Biomolecular Solutions by All-atom and Implicit-Solvent Calculations. 1st Panhellenic Meeting on Biological Physics. November 30 2007, National Hellenic Research Foundation, Athens.

24.  A residue-pairwise Generalized Born approximation, suitable for protein design simulations. CHARMM developers meeting, July 21-23 2006, Harvard University, USA.

25.  Conformational Analysis of Compstatin with Molecular Dynamics Simulations in Explicit Water. Symposium From Computational Biophysics to Systems Biology 2006”, June 6-9 2006, Juelich, Germany; Presented by P. Tamamis.

26.  Catalytic inhibition of Glycogen Phosphorylase: Insights from  Molecular Dynamics Free Energy Simulations. International Society of Quantum Biology and Pharmacology, Presidents meeting, June 24-27 2006, Strasbourg, France.

27.  Conformational Investigation of Amyloidogenic Peptidic Analogues of Chorion Proteins. CECAM meeting on Protein Aggregation, May 22-25 2006, Lyon France.

28.  Attraction of Iodide Ions by the Free Water Surface Revealed by Simulations with a Polarizable Force Field, Based on Drude Oscillators. CHARMM developers meeting, July 7-9 2005, Cornell University Medical School, USA.

29.  The effect of Proton Binding on Protein Stability. Insights from MD Simulations and Continuum Models. XXI Hellenic Conference on Solid-State Physics, Nicosia, August 28-31 2005.

30.  Proton Binding to Proteins. Insights from Continuum Models with a Linear Response Approximation. International Conference of Computational Methods in Sciences and Engineering, Loutraki, October 21-25, 2005.

31.  Continuing Challenges in Free Energy Calculations: Theory and Applications in Chemistry and Biology.  CECAM meeting, 12-14 May 2004, Lyon, France.

32.  Understanding Protein-Small Molecule Interactions With Molecular Dynamics Simulations and Continuum Electrostatics Calculations. 3rd International Multidisciplinary Workshop on the Self-Assembly of Proteins and Peptides, August 1-5 2003, Herakleion Crete.

33.  Free Energy Calculations: Modern Applications to the Understanding of Protein Specificity and to the Design of new Ligands”. 1st Congress of the Greek Crystallographic Society, May 17-18 2002, Athens, Greece.

34.  Specificity of Native and Engineered Aspartyl-tRNA Synthetase: Insights from Atomic Simulations and Continuum Electrostatics Models.  CECAM workshop on Electrostatics for Complex Molecular Systems: Continuum Models and Beyond”. June 18-20 2001, Lyon, France.

35.  Studies of Protein Specificity by Atomic-detail Simulations and Continuum Electrostatics Models. February 7, 2001, Institute of Physical Chemistry, Demokritos National Center for Scientific Research, Athens, Greece.

36.  Physics inspired by Biology. December 15, 2000, Department of Physics, University of Athens.

37.  The Effect of Mutation K198L on the Specificity of Aspartyl-tRNA Synthetase: Insights From Poisson-Boltzmann and Molecular Dynamics Calculations. CECAM workshop on Challenges in Free Energy Calculations”. June 19-21 2000, Lyon, France.

 

Publications in Refereed International Journals

 

Citations in braces [..]; 41 publications; 2270 citations on 09/2013, ISI Web of Science); 55.48 citations/publication; h=20;  * marks corr. Author.

 

1.     P. Tamamis, E. Kassotakis, G. Archontis*, A. Mitraki* (2013). [0 citations]. Combination of theoretical and experimental approaches for the design and study of fibril-forming peptides.

Protein Design: Methods and Applications, 2nd Edition. Humana Press.

2.     T. Simonson*, T. Gaillard, D. Mignon, M. Schmidt am Busch, A. Lopes, N. Amara, S. Polydorides, A. Sedano, K. Druart, G. Archontis (2013). [0 citations]  Computational Protein Design: The Proteus Software and Selected Applications. Journal of Computational Chemistry 34:2472-2484.

3.     F. Ioannou, E. Leontidis*, G. Archontis* (2013). [0 citations]. Helix Formation by Alanine-based Peptides in Pure Water and Electrolyte Solutions: Insights from Molecular Dynamics Simulations.

Journal of Physical Chemistry B 117:9866-9876.

4.     R. D. Gorham, D. L. Forest, P. Tamamis, A. Lopez de Victoria, M. Kraszni, C. A. Kieslich, C. D. Banna, M. L. Bellows-Peterson, C. K. Larive, C. A. Floudas, G. Archontis, L. V. Johnson*, D. Morikis* (2013). [0 citations]. Novel Compstatin Family Peptides Inhibit Complement Activation by Drusen-like Deposits in Human Retinal Pigmented Epithelial Cell Cultures.

Experimental Eye Research 116:96-108.   

5.     C. A. Kieslich, P. Tamamis, R. D. Gorham Jr., A. L. De Victoria, N. U. Sausman, G. Archontis*, D. Morikis* (2012) [0 citations]. Exploring Protein-Protein and Protein-Ligand Interactions in the Immune System using Molecular Dynamics and Continuum Electrostatics.

Current Physical Chemistry (in Press).

6.     P. Tamamis, A. L. de Victoria, R. D. Gorham, M. L. Bellows-Peterson, P. Pierou, C. A. Floudas*, D. Morikis*, G. Archontis* (2012). [0 citations] Molecular Dynamics in Drug Design: New Generations of Compstatin Analogs.  

Chemical Biology & Drug Design 79:703-718.

7.     F. Ioannou, G. Archontis* and E. Leontidis* (2011) [1 citation]. Specific Interactions of Sodium Salts With Alanine Dipeptide and Tetrapeptide in Water: Insights from MD Simulations.

Journal of Physical Chemistry B 115:13389-13400.

8.     P. Tamamis and G. Archontis* (2011) [1 citation]. 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.

9.     P. Tamamis, P. Pierou, C. Mytidou, CA. Floudas*, D. Morikis* and G. Archontis* (2011) [1 citation]. Design of a Modified Mouse Protein with Ligand Binding Properties of its Human Analog using Molecular Dynamics Simulations: The Case of C3 Inhibition by Compstatin. Proteins: Structure, Function and Bioinformatics, under review.

10.  S. Polydoridis, N. Amara, C. Aubard, P. Plateau, T. Simonson* and G. Archontis* (2011) [1 citation]. Computational protein design with a generalized Born solvent model: application to Asparaginyl-tRNA synthetase. Proteins: Structure, Function and Bioinformatics, In Press; Special Issue in protein electrostatics.

11.  G. Pieridou, C. Avgousti-Menelaou, P. Tamamis, G. Archontis and S. Hayes* (2011) [0 citations]. UV Resonance Raman Study of TTR(105−115) Structural Evolution as a Function of Temperature.

J. Phys. Chem. B 115:4088-4098.

12.  J. Hayes*, V. T. Skamnaki, G. Archontis, C. Lamprakis, K. Sarrou, N. Bischler, A-L. Skaltsounis, S. E. Zographos, N. G. Oikonomakos (2011) [6 citations]. 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: Structure, Function and Bioinformatics 79:703-719.

13.  A. Aleksandrov, S. Polydoridis, G. Archontis* and T. Simonson* (2010) [4 citations]. Predicting the Acid/Base Behavior of Proteins: A Constant-pH Monte Carlo Approach with Generalized Born Solvent.

J. Phys. Chem. B. 114:10634-10648.

14.  P. Tamamis, D. Morikis*, C.A. Floudas* and G. Archontis* (2010) [5 citations]. Species Specificity of the Complement Inhibitor Compstatin Investigated by All-atom Molecular Dynamics simulations. Proteins; Structure, Function and Bioinformatics 78:2655-2667.

15.   P. Tamamis, E. Kasotakis, A. Mitraki and G. Archontis* (2009) [6 citations]. Amyloid-like Self-Assembly of Peptide Sequences from the Adenovirus Fiber Shaft: Insights from MD Simulations. J. Phys. Chem. B. 113:15639-15647.

16.  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) [659 citations]. CHARMM. The Biomolecular Simulation Program. Special Issue, J. Comp. Chem. 30:1545-1615.

17.  P. Tamamis, L-A. Abramovich, M. Reiches, K. Marshall, P. Sikorski, L. Serpell, E. Gazit and G. Archontis* (2009) [22]. Self-Assembly of Phenylalanine Oligopeptides: Insights from Experiments and Simulations. Biophys. J. 96:5020.

18.  M. Benitifa, 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) [21 citations]. Glucose-based spiro-isoxazolines: A new family of potent glycogen phosphorylase inhibitors. Bioorganic and Medicinal Chemistry 17:7368-7380.

19.  K-M. Alexacou, J.M Hayes, C. Tiraidis, S.E. Zographos, D.D. Leonidas, E.D. Chrysina, G. Archontis and N.G. Oikonomakos (2008) [16 citations]. Crystallographic studies on N-(β-D-glucopyranosyl)-4-phenyl-1,2,3-triazoleacetamide, an inhibitor of glycogen phosphorylase: Proteins, Structure, Function and Bioinformatics 71:1307-1323.

20.  P. Tamamis, S.S. Skourtis, D. Morikis, J.D. Lambris and G. Archontis* (2007) [7 citations]. Conformational analysis of Compstatin analogues with Molecular Dynamics Simulations in Explicit Water. J. Mol. Graph. Model. 26: 571.

21.  S. Polydoridis, D.D. Leonidas, N.G. Oikonomakos and G. Archontis* (2007) [6 citations]. Recognition of RNAse A by 3’-5’-Pyrophosphate-linked Dinucleotide Inhibitors: A Molecular Dynamics/Continuum Electrostatics Analysis. Biophys. J. 92:1659.

22.  A. Lopes, A. Alexandrov, C. Bathelt, G. Archontis* and T. Simonson* (2007) [17 citations]. Computational sidechain placement and protein mutagenesis with implicit solvent models. Proteins: Structure, Function and Bioinformatics 67:853.

23.  G. Archontis* and E. Leontidis (2006) [16 citations]. Dissecting the stabilization of iodide at the air-water interface into components: A free energy analysis. Chem. Phys. Lett. 420:199.

24.  G. Archontis* and T. Simonson* (2005) [14 citations]. A residue-pairwise Generalized Born scheme suitable for protein design calculations. J. Phys. Chem. B 109:22667.

25.  G. Archontis*, E. Leontidis* and G. Andreou (2005) [37 citations]. Attraction of Iodide Ions by the Free Water Surface Revealed by Simulations with a Polarizable Force Field, Based on Drude Oscillators. J. Phys. Chem. B, 109:17957.

26.  G. Archontis*, K. Α. Watson, Q. Xie, G. Andreou, E. Chrysina, S.E. Zographos, N.G. Oikonomakos, L.N. Johnson and M. Karplus* (2005) [21 citations]. Molecular Recognition and Relative Binding of Glucopyranose Spirohydantoin Analogues to Glycogen Phosphorylase: A Free Energy Perturbation Study. Proteins: Structure, Function and Bioinformatics 61:984.

27.  Κ.Α. Watson, E.D. Chrysina, K.E. Tsitsanou, S.E. Zographos, D.D. Leonidas, G.W.J. Fleet, G. Archontis, and N.G. Oikonomakos, (2005) [21 citations]. Kinetic and crystallographic studies of glucopyranose spirohydantoin and glucopyranosylamine analogues inhibitors of glycogen phosphorylase. Proteins: Structure, Function and Bioinformatics, 61:966.

28.  G. Archontis* and T. Simonson* (2005) [37 citations]. Proton binding to proteins: A self-consistent dielectric continuum analysis. Biophys. J. 88:3888.

29.  N.G. Oikonomakos*, S.E. Zographos, V.T. Skamnaki, and G. Archontis (2002) [21 citations]. The 1.76 A resolution crystal structure of glycogen phosphorylase b, complexed with glucose and CP320626, a potential antidiabetic drug. Bioorg. Med. Chem. 10: 313.

30.  T. Simonson, G. Archontis and M. Karplus* (2002) [203 citations]. Protein-ligand recognition: Free-energy simulations come of age. Acc. Chem. Res. 35, 430.

31.  G. Archontis* and T. Simonson (2001) [36]. Dielectric relaxation in an enzyme active site. J. Am. Chem. Soc. 123, 11047.

32.  G. Archontis, T. Simonson and M. Karplus* (2001) [70]. Binding free energies and free energy components from MD and PB calculations. Application to aminoacid recognition by Aspartyl-tRNA synthetase. J. Mol. Biol. 306:307.

33.  S. Skourtis, G. Archontis and Q. Xie (2001) [30 citations]. Electron transfer through fluctuating bridges: On the validity of the superexchange mechanism and time-dependent tunneling matrix elements. Journal of Chemical Physics 115:9444-9462.

34.  Q. Xie, G. Archontis and S. Skourtis (1999) [32 citations]. Protein electron transfer: A numerical study of tunneling through fluctuating bridges. Chemical Physics Letters 312(2­4):237­246 .

35.  T. Simonson, G. Archontis and M. Karplus (1999) [69 citations]. A Poisson­Boltzmann study of charge insertion in an enzyme active site: the effect of dielectric relaxation. Journal of Physical Chemistry B 103:6142­6156.

36.  G. Archontis, T. Simonson, D. Moras and M. Karplus (1998) [57 citations]. Specific amino acid recognition by Aspartyl­tRNA synthetase, studied by free energy simulations. Journal of Molecular Biology 275:823­846.

37.  T. Simonson, G. Archontis and M. Karplus (1997) [84 citations]. Continuum treatment of long­range interactions in free energy calculations. Application to protein­ligand binding. Journal of Physical Chemistry B 101:8349­8362.

38.  G. Archontis and M. Karplus (1996) [30 citations]. Cumulant expansion of the free energy: application to free energy derivatives and component analysis. Journal of Chemical Physics 105: 11246­11260.

39.  T. Lazaridis, G. Archontis and M. Karplus (1995) [137 citations]. The enthalpic contribution to protein stability: Insights from atom­based calculations and statistical mechanics. Advances in Protein Chemistry 47:231-296.

40.  G. Z. Archontis and E.I. Shakhnovich (1994) [7 citations]. Phase transitions in heteropolymers with ``secondary structure''. Physical Review E 49;3109­3123.

41.  S. Boresch, G. Archontis and M. Karplus (1994) [94 citations]. Free energy simulations: The meaning of the individual contributions from a component analysis. Proteins: Structure, Function and Genetics 20:25­33.