Faculty

Short CV of Professor Stavros J. Hamodrakas

Personal:

Name: Stavros J. Hamodrakas
Birth: March 10, 1947
Place: Kalamata, Greece

Address: Faculty of Biology,
Department of Cell Biology and Biophysics
University of Athens, Athens 15701
Greece
Phone: +30-210-7274931
Fax: +30-210-7274254
e.mail: shamodr@biol.uoa.gr
web: http://biophysics.biol.uoa.gr , http://bioinformatics.biol.uoa.gr/msc

Present Positions:

• Professor and Head, Department of Cell Biology & Biophysics, Faculty of Biology, University of Athens
• Director, MSc "BIOINFORMATICS" course, Faculty of Biology, University of Athens (http://bioinformatics.biol.uoa.gr/msc/en/general.html)
• Director, MSc “Applications of Biology in Medicine”, Faculty of Biology & School of Medicine, University of Athens
• President of the Hellenic Society for Computational Biology & Bioinformatics (http://www.hscbb.gr/people)

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• Education
• Research Interests
• Research Experience
• Teaching Experience
• Other Activities
• List of publications

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  Education:

  1970-1974, Ph.D Astbury Dept. of Biophysics, University of Leeds, U.K

  1965-1970, B.Sc Physics Dept., University of Athens, Greece 

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  Research Interests:

  The scientific research interests of our laboratory are focused in the fields of Structural Biology / Molecular Biophysics and Computational Biology / Bioinformatics. More specifically, we are dealing with:
• Studies of water soluble, globular protein structure, function and interactions with small molecules, aiming at the determination of the mechanisms of molecular recognition at/or near atomic resolution. Model systems of study include: a) the interactions of the lectin concanavalin A (conA) with saccharides and hydrophobic molecules, b) the enzyme DHFR and its interactions with inhibitors, which act as antibacterial and anticancer agents.
• Development of algorithms that predict the structure, function and interaction of proteins from sequence alone. These algorithms frequently have genome-wide applications. The knowledge expertise of our team, in combination with the sophisticated tools that we develop, enables us to build curated, expert, knowledge-based, relational protein and DNA biological databases. Recently, special emphasis is given to the development of methods and software for the prediction of structure, function and interactions of transmembrane proteins and the development of relational, object oriented databases of transmembrane proteins. We are mainly focused on the GPCRs - G-protein - Effectors system and on the outer membrane proteins (OMPs) of Gram-negative bacteria, which are both of great pharmacological interest. Unique, worldwide, relational databases of GPCRs - G-protein - Effectors interactions and also a database of OMPs, are freely accessible through the Internet.
• Structural and self-assembly studies of fibrous proteins, which form extracellular, proteinaceous structures of great physiological importance like lepidopteran, dipteran and fish chorions. Model structures of silkmoth chorion proteins and their interactions have been proposed. Also, we are studying chitin-protein interactions for the formation of arthropod cuticle. We have recently proposed a model structure of cuticular proteins and we developed a universal, freely available through the Internet, cuticular protein relational database.
• Structural and self-assembly studies of silkmoth chorion peptide analogues as novel self-assembled polymers with amyloid properties are performed and they may lead to the construction of new biomaterials with extraordinary physical properties. We determined that silkmoth chorion is a natural, protective amyloid and we proposed, for the first time worldwide, the existence of natural, functional amyloids.  We also currently experimentally studying a great variety of amyloidogenic determinants (aggregation-prone) peptides predicted by our AMYLPRED prediction algorithm in several widespread and also rare pathological amyloidoses.

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Research Experience:

1976-present	Faculty of Biology, University of Athens
2008	1 month visit, University of Colorado at Boulder, USA 1 month visit, EMBL, Heidelberg, Germany
2007	1 month visit, University of Colorado at Boulder, USA
2006	1 month visit, EMBL, Heidelberg, Germany
2005	1 month visit, EMBL, Heidelberg, Germany
2004	1 month visit, EMBL, Heidelberg, Germany
2003	1 month visit, EMBL, Heidelberg, Germany
2002	1 month visit, EMBL, Heidelberg, Germany
2001	1 month visit, EMBL, Heidelberg, Germany
2000	1 month visit, EMBL, Heidelberg, Germany
1999	1 month visit, EMBL, Heidelberg, Germany
1998	2 month visit, EMBL, Heidelberg, Germany
1995-96	5 month visit, EMBL, Heidelberg, Germany
1994-95	3 month visit, EMBL, Heidelberg, Germany
1994	3 month visit Dept. of Biochemistry University of Mississippi, USA
1990-91	7 month visit, Dept. of Medical Biophysics University of Toronto, Canada
1987	1 month visit, EMBL, Heidelberg, Germany
1985	2 months visit, EMBL, Heidelberg
1984	1 month visit, Astbury Dept. Biophysics, U.K
1983	2 months visit, EMBL, Heidelberg
1982	2 months visit, EMBL, Heidelberg
1980	1 month visit , EMBL, Heidelberg 15 days visit, MRC, Cambridge, U.K
1979	2 months visit , Rosenstiel Basic Medical Sciences Research Center, Brandeis University, USA and the Biological Laboratories, Harvard University, USA
1977	2 months visit , Astbury Dept. of Biophysics, Leeds University, U.K
1976	Environmental Pollution Control Project for Athens (4 months as a research assoc.)
1975-1976	Nuclear Research Center "Demokritos", Athens, Greece (Research Scientist)
1970-1974	Astbury Dept. of Biophysics, University of Leeds, U.K (research assistant)

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Teaching Experience:

• COURSES (UNDERGRADUATE level)
  • I am teaching a full (one semester) ‘BIOPHYSICS’ course to 3rd year Biology and Physics students, since 1977.
  • I am also teaching a full (one semester) ‘BIOINFORMATICS’ course to 3rd year Biology students, since 1986.
  • I was a visiting professor of a full (one semester) ‘BIOPHYSICS’ course, at the Department of Medicine of the University of Crete, Heraclion, Crete, for two consecutive years, 1984 and 1985.
  
  
• COURSES (POSTGRADUATE level) I am participating (to various extents, ranging from 10-80%) in the teaching of the following courses of the MSc course ‘BIOINFORMATICS’, since 2003
  • BIOMOLECULAR STRUCTURE AND FUNCTION
  • PRINCIPLES AND METHODS IN BIOINFORMATICS
  • COMPUTATIONAL ANALYSIS OF BIOMACROMOLECULAR SEQUENCES
  • COMPUTATIONAL ANALYSIS OF BIOMOLECULAR STRUCTURES
  • MOLECULAR RECOGNITION - MOLECULAR DISEASES - STRUCTURAL DRUG-DESIGN
  • METHODOLOGY OF RESEARCH
  
  
• SUPERVISION OF PhD, MSc and Undergraduate students I was the supervisor of nine (9) PhD students, who completed their PhD’s and I am currently supervising two (2) students, carrying out their PhD’s.
  I have supervised more than 25 MSc Diploma Theses and more than 150 Undergraduate Diploma Theses
  I was also an external examiner to more than 20 PhD Theses
  
  
• BOOKS – MONOGRAPHS
  • Hamodrakas, S.J. ‘Molecular Biophysics’ (in Greek, 1st edition 1987, 2nd edition 1993), “SYMMETRIA” (publishers).
    This book contains topics on:
    
    1. X-ray Diffraction studies of Biological Micro- and Macromolecules
    2. Applications of Neutron Diffraction in Studies of BiologicalStructures
    3. Use of Molecular Models- Conformational Analysis of Biomolecules using Energy Calculations and modeling
    4. Principles of Stereochemistry. Applications in Biomolecules and Biological Structures
    5. Principles of Protein Structure
    6. Protein Folding and Structure Prediction
    7. The structure of Fibrous Proteins
    8. Image Analysis- Optical Diffraction and Reconstruction- 3D-reconstruction of Biological Structures from Electron Micrographs
    9. Principles and Applications of Infrared Spectroscopy, Laser-Raman spectroscopy, NMR spectroscopy, O.R.D and C.D spectroscopy in studies of biomolecules and biological structures
    10. Molecular Recognition: Structure and Function of biomicromolecules (drugs, neurotransmitters, antibiotics e.t.c) and their receptors
    11. Photoreceptors: Rhodopsin and Bacteriorhodopsin (structure and function)
    
    
  • Hamodrakas, S.J. et al. ‘Bioinformatics practicals’ (in Greek) (2002) http://biophysics.biol.uoa.gr/courses/bioinformatics/
  • "BIOINFORMATICS: a practical guide to the analysis of genes and proteins" (2nd Edition) A.D. Baxevanis & B.F.F. Quelette (eds.) Authorized translation in Greek from the English language edition (John Wiley & Sons, Inc.) E.N. Moudrianakis & S.J. Hamodrakas (eds.) Parisianou Publishers (2004.
  • Introduction to Protein Structure (2nd Edition) Branden, C. & Tooze, J. Authorized translation in Greek from the English language edition, Glykos, E.N., Kokkinidis, M., Hamodrakas, S.J., Tsernoglou, D. (eds.), Basdra, I. Publishers. (2006)
  • Hamodrakas, S. J. (1992) Molecular architecture of helicoidal proteinaceous eggshells in "Results and Problems in Cell Differentiation", Vol. 19, (S.T. Case ed.), Ch. 6, pp. 116-186. Springer-Verlag, Berlin-Heidelberg.
  • Willis, J.H., Iconomidou, V.A., Smith, R.F. and Hamodrakas, S.J. (2005) Cuticular Proteins in 'Comprehensive Insect Science', (L. I. Gilbert, K. Iatrou, and S. Gill, Eds.), Elsevier, Oxford, Vol. 4, Ch. 2:79-110.
  • Sgourakis, N.G., Bagos, P.G., Hamodrakas, S.J. (2009) Computational methods for the prediction of GPCRs coupling selectivity, 2008, in ‘Handbook of Research on Systems Biology Applications in Medicine’, (A. Daskalaki, Eds.), Medical Information Science, Vol. I, Ch. 9: 167-181.
  • Bagos, P.G., Hamodrakas, S.J. (2009) Bacterial beta-barrel outer membrane proteins: A common structural theme implicated in a wide variety of functional roles in ‘Handbook of Research on Systems Biology Applications in Medicine’, (A. Daskalaki, Eds.), Medical Information Science, Vol. I, Ch. 10: 182-207.
  • Hamodrakas, S.J., Iconomidou, V.A. (2010) Silkmoth chorion: A natural protective amyloid (Ch. 7) in ‘THE FUNCTIONAL FOLD: Amyloid Structures in Nature’ (Suzi Jarvis & Anika Mostaert, eds.) ISBN 978-981-4267-40-3, Pan Stanford Publishing.
  • Iconomidou, V.A., Hamodrakas, S.J. (2010) Silkmoth chorion proteins: A protective role for amyloid (Ch. 5) in ‘Functional amyloid aggregation’ (Stefania Rigacci and Monica Bucciantini eds.), Research Signpost (publishers).

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Other Activities:

• EXTERNAL FUNDING – RESEARCH GRANTS Coordinator of more than 20 research projects funded by the private sector or by National and EU sources (with a total budget of ~ 3M Euros)
  
  
• HONORS & AWARDS 1965-1970 IKY Fellowship
  1970-1974 Research Assistant, Astbury Dept. of Biophysics, University of Leeds, UK
  1979 Greek Ministry of Coordination Fellowship (visits to Harvard & Brandeis Universities)
  1980 EMBO Short Term Fellowship
  1982 EMBO Short Term Fellowship
  1983 EMBO Short Term Fellowship
  1985 EMBO Short Term Fellowship
  1987 EMBO Short Term Fellowship
  1995-1996 SRMB (Supercomputing Resources in Molecular Biology) Fellowship
  
  
• PROFESSIONAL AFFILIATIONS AND ACTIVITIES
  • Reviewer to Scientific Journals “Computer Applications in the Biosciences (CABIOS)”, “Bioinformatics”, “Proteins”, “Protein Engineering”, “J. Structural Biology”, “BMC Bioinformatics”, “FEBS Letters”, “Nucleic Acids Research”, “International Journal of Biological Macromolecules”, “Biophysical Journal”, “Journal of Proteome Research”, “Biopolymers”, “PlOS One”, “J. Biol. Chemistry”, “Insect Biochem. Mol. Biol.”, “J. Mol. Biol.”, etc.
  • Editor or Associate Editor to Scientific Journals “BMC Bioinformatics”, “Advances in Bioinformatics”, “Open Applied Informatics Journal”, “Advanced Studies in Biology”, “J. Biomedicine and Biotechnology”
  • Member of Scientific Societies
    • Hellenic Society for Biological Sciences (EEBE)
    • Hellenic Biochemical and Biophysical Society
    • International Union of Crystallographers
    • Hellenic Crystallographic Association (HECRA)
    • British Biophysical Society
    • Founding member and current President of the Hellenic Society for Computational Biology and Bioinformatics
    I was the General Secretary of EEBE for six years (1988-1993)
  • Expert/Reviewer in International/National Organisms
    • Representative of Greece, C.E.E.-U.L.B. meeting on "Computational resources for Protein Engineering", Brussels (1985).
    • Representative of Greece, meeting on “Informational Technology of CGC Biotechnology”, E.C, Brussels (1988).
    • Representative of Greece to the edition of the “1994 Report on Protein Engineering R&D Programmes in Europe” of Å.C (E.U), after several meetings during the period 1993-1994, at Brussels.
    • Representative of Greece for the creation of the “pilot” programme “Coordination of Structural Biology in Europe: National, EC and Industry Joint Efforts” of Å.C (E.U), after several meetings during the period 1995-1997, at Brussels.
    • Reviewer of several grant proposals of G.S.R.T (General Secretariat of Research & Technology of Greece) and of Greek Universities.
  
  
• NATIONAL & INTERNATIONAL CONFERENCES More than 50 abstracts and 20 talks in International Conferences and more than 180 abstracts in National Conferences. I was a member of the Organizing Committee of, at least, 8 International and National Conferences. More than 1200 citations to my publications and an h-index=21.
  
  

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  List of publications:

  (PDF's available HERE )
  1. Hamodrakas, S. J., Geddes, A. J. and Sheldrick, B. (1974) X-ray analysis of disodium cromoglycate, Journal of Pharmacy and Pharmacology, 26, 54.
  2. Hamodrakas, S. J., Geddes, A. J. and Sheldrick, B. (1974) The crystal structure of β-methylphenylcholine ether bromide, Acta Cryst., B30, 881.
  3. Geddes, A. J., Hamodrakas, S. J. and Sheldrick, B. (1974) (The crystal structure of) N-acetyl methionine methyl ester, C8H15NO3S, Cryst. Struct. Comm., 3, 97.
  4. S. J. Hamodrakas (1974) X-ray crystallographic studies of disodium cromoglycate, β-methylphenylcholine ether bromide and N-acetyl methionine methyl ester, Ph.D Thesis, University of Leeds (U.K).
  5. Hamodrakas, S. J., Filippakis, S. E. and Sheldrick, B. (1977) (The crystal structure of) 2-carboxamidomethyl-4,5-dimethoxy-phenyl diethyl sulfonamide, C14H22N2O5S, Cryst. Struct. Comm., 6, 209.
  6. Hamodrakas, S. J. and Filippakis, S. E. (1977) (The crystal structure of) N-morpholine-4,5 dimethoxy-2-carboxymethyl benzene sulfonamide, C14H19NO7S, Cryst. Struct. Comm., 6, 301.
  7. Hamodrakas, S. J., Akrigg, D. and Sheldrick, B. (1978) (The crystal structure of) Methyl dehydroabietate, C21H30O2, Cryst. Struct. Comm., 7, 429.
  8. Hamodrakas, S. J., Akrigg, D., Sheldrick, B. and Camoutsis, C. (1978) (The crystal structure of) Ethyl-3-[4,5-Dimethoxy-2-(5-methyl-2pyridylsulfamoyl) phenyl] propionate, Acta Cryst., B34, 3426.
  9. Hamodrakas, S. J., Margaritis, L. H. and Nixon, P. E. (1982) Crystalline layer in Drosophila melanogaster eggshell: Arrangement of components as revealed by negative staining and reconstruction, Int. J. Biol. Macromol., 4, 25-31.
  10. Hamodrakas, S. J., Jones, C. W. and Kafatos, F. C. (1982) Secondary structure predictions for silkmoth chorion proteins, Biochim. Biophys. Acta, 700, 42-51.
  11. Hamodrakas, S. J., Asher, S. A., Mazur, G. D., Regier, J. C. and Kafatos, F. C. (1982) Laser-Raman studies of protein conformation in the Silkmoth chorion, Biochim. Biophys. Acta , 703, 216-222.
  12. Regier, J. C., Kafatos, F. C. and Hamodrakas, S. J. (1983) Silkmoth chorion multigene families constitute a superfamily:Comparison of C and B family sequences, Proc. Natln. Acad. Sci. USA, 80, 1043-1047.
  13. Hamodrakas, S. J., Paulson, J. R., Rodakis, G. C. and Kafatos F. C. (1983) X-ray Diffraction studies of a silkmoth chorion, Int. J. Biol. Macromol., 5, 149-153.
  14. Eliopoulos, E. E., Sheldrick, B. and Hamodrakas, S. J. (1983) The crystal structure of Ethyl 3-[4,5-Dimethoxy-2-(4- methyl-2-pyridylsulfamoyl)phenyl] propionate, C19H24N2O8S, Acta Cryst., C39, 743.
  15. Eliopoulos, E. E., Sheldrick, B. and Hamodrakas, S. J. (1983) The crystal structure of Ethyl 3-[4,5-Dimethoxy-2-(3-methyl-2-pyridylsulfamoyl)phenyl] propionate), C19H24N2O8S, Acta Cryst., C39, 1693.
  16. Margaritis, L. H., Hamodrakas, S. J., Arad, T. and Leonard, K. R. (1984) Three Dimensional Reconstruction of Innermost Chorion Layer from Drosophila melanogaster, Biol. Cell, 52 (3), 279-284.
  17. Hamodrakas, S. J. (1984) Twisted β-pleated sheet: The Molecular Conformation which possibly dictates the formation of the Helicoidal Architecture of several proteinaceous eggshells, Int. J. Biol. Macromol., 6, 51.
  18. Hamodrakas, S. J. and Kafatos, F. C. (1984) Structural Implications of Primary Sequences from a family of Balbiani Ring-Encoded Proteins in Chironomus, J. Mol. Evol., 20, 296-303.
  19. Hamodrakas, S. J., Kamitsos, E. I. and Papanicolaou, A. (1984) Laser-Raman spectroscopic studies of the Eggshell (Chorion) of Bombyx mori, Int. J. Biol. Macromol., 6, 333-336.
  20. Hamodrakas, S. J., Etmektzoglou, Th. and Kafatos, F. C. (1985) Amino acid Periodicities and Their Structural Implications for the Evolutionarily Conservative Central Domain of Some Silkmoth Chorion Proteins, J. Mol. Biol., 186, 583-589.
  21. Hamodrakas, S. J., Margaritis, L. H., Papassideri, I. and Fowler, A. (1986) Fine structure of the silkmoth Antheraea polyphemus chorion as revealed by X-ray diffraction, and freeze fracturing, Int. J. Biol. Macromol., 8, 237-242.
  22. Papanicolaou, A., Margaritis, L. H. and Hamodrakas, S. J. (1986) Ultrastructural analysis of chorion formation in the silkmoth Bombyx mori, Can. J. Zool., 64, 1158-1173.
  23. Hamodrakas, S. J., Kamitsos, E. I. and Papadopoulou, P. (1987) Laser-Raman and infrared spectroscopic studies of protein conformation in the eggshell of the fish Salmo gairdneri, Biochim. Biophys. Acta, 913, 163-169.
  24. Hamodrakas, S. J. (1988) A protein secondary structure prediction scheme for the IBM-PC and compatibles, Computer applications in the Biosciences, 4 (4), 473-477.
  25. Hamodrakas, S. J., Bosshard, H. E. and Carlson, C. N. (1988) Structural models of the evolutionarily conservative central domain of silkmoth chorion proteins, Protein Engineering, 2 (3), 201-207.
  26. Hamodrakas, S. J., Alexandraki, E., Troganis, A. and Stassinopoulou, C.I. (1989) Models of binding of 4'-nitrophenyl β-D-mannopyranoside to the lectin concanavalin A, Int. J. Biol. Macromol., 11 (1), 17-22.
  27. Hamodrakas, S. J., Batrinou, A. and Christophoratou, T. (1989) Structural and functional features of Drosophila chorion proteins s36 and s38 from analysis of primary structure and infrared spectroscopy, Int. J. Biol. Macromol., 11 (5), 307-313.
  28. Eliopoulos, E., Sheldrick, B. and Hamodrakas, S. J. (1991) (The crystal structure of) 4,5-Dimethoxy-2-[3-(1,4-oxazinan-4-yl)-3-oxopropyl]-N-(2-pyridyl)-benzenesulfonamide Methanol solvate, Acta Cryst., C47, 1212-1215.
  29. Aggeli, A., Hamodrakas, S. J., Komitopoulou, K. and Konsolaki, M. (1991) Tandemly repeating peptide motifs and their secondary structure in Ceratitis capitata eggshell proteins Ccs36 and Ccs38, Int. J. Biol. Macromol., 13, 307-315.
  30. Margaritis, L. H., Hamodrakas, S. J., Papassideri, I. Arad, T. and Leonard, K. R. (1991) Three-dimensional reconstruction of innermost chorion layer of Drosophila grimshawi and Drosophila melanogaster eggshell mutant fs(1)384, Int. J. Biol. Macromol., 13, 247-253.
  31. Orfanidou, C. C., Hamodrakas, S. J., Margaritis, L. H., Galanopoulos, V.K., Dedieu, J. C., and Gulik-Krzywicki, T. (1992) Fine structure of the chorion of Manduca sexta and Sesamia nonagrioides as revealed by scanning electron microscopy and freeze-fracturing, Tissue & Cell, 24(5), 735-744.
  32. Wellman, S. E., Hamodrakas, S. J., Kamitsos, E. I.?and Case, S. T. (1992) Secondary structure of synthetic peptides derived from the repeating unit of a giant secretory protein from Chironomus tentans, Biochim. Biophys. Acta, 1121, 279-285.
  33. Gessman, R., Petratos, K., Hamodrakas, S. J., Tsitsa, P. and Antoniadou-Vyza, E. (1992) Structure of 2-Amino-6-dimethylamino-4-(tricyclo [3.3.1.1.3,7] decyl-1-yl)-1,3,5-triazine, Acta Cryst., C48, 347-350.
  34. Hamodrakas, S. J., Hempel, A., Camerman, N., Ottensmeyer, F. P., Tsitsa, P., Antoniadou-Vyzas, E. and Camerman, A. (1992) Molecular and crystal structure of 2-amino-4-(tricyclo[3.3.1.1.3,7] decyl-1)-6-N-methyl-piperazino-1,3,5-triazine, J. Cryst. Spectrosc. Res., 22, 607-614.
  35. Hamodrakas, S. J. (1992) Molecular architecture of helicoidal proteinaceous eggshells in "Results and Problems in Cell Differentiation", Vol. 19, (S.T. Case ed.), Ch. 6, pp. 116-186 Springer-Verlag, Berlin-Heidelberg (rev. article).
  36. Hempel, A., Camerman, N., Hamodrakas, S. J., Ottensmeyer, F. P., Troganis, A., Stassinopoulou, C. I. and Camerman, A. (1993) 2,2,6,6-Tetramethylpiperidine-1-oxyl-4-yl-β-D-glucopyranoside, Acta Cryst., C49, 298-300.
  37. Kolocouris, A., Kolocouris, N., Foscolos, G. B., Fytas, G., Hempel, A., Camerman, N., Camerman, A. and Hamodrakas, S. J. (1993) Molecular and crystal structures of a tricyclic β-lactam ketone and its Mannich base, J. Cryst. Spectrosc. Res., 23, 663-668.
  38. Tsitsa, P., Antoniadou-Vyza, E., Hamodrakas, S. J., Eliopoulos, E. E., Tsantili-Kakoulidou, A., Lada-Hytiroglou, E., Roussakis, C., Chinou, I., Hempel, A., Camerman, N., Ottensmeyer, F. P., and Van den Berghe, D. A. (1993) Synthesis, Crystal Structure and Biological Properties of a new Series of Lipophilic s-Triazines, Dihydrofolate Reductase (DHFR) Inhibitors, Eur. J. Med. Chem., 28, 149-158.
  39. Perrakis, A., Hempel, A., Hamodrakas, S. J., Camerman, N., Tsitsa, P., Antoniadou-Vyzas E. and Camerman, A. (1993) Molecular and crystal structure of 2-amino-6-dimethyl amino-4-(-tricyclo[3.3.1.13,7]dec-1-yl) methyl-1,3,5-triazine, J. Cryst. Spectrosc. Res., 23, 821-824.
  40. Perrakis, A., Constantinides, C., Athanasiades, A. and Hamodrakas, S. J. (1995) PBM: A software package to create, display and manipulate interactively models of small molecules and proteins on IBM-compatible, PCs Computer Applications in the Biosciences (CABIOS), 11(2), 141-145.
  41. Orfanidou, C. C., Chryssikos, G. D., Kamitsos, E. I., Wellman, E., Case, S. T. and Hamodrakas, S. J. (1995) Spectroscopic studies of Manduca sexta and Sesamia nonagrioides chorion protein structure, Int. J. Biol. Macromol., 17(2), 93-98.
  42. Hamodrakas, S. J., Perrakis, A. and Antoniadou-Vyzas, E. (1996) A de novo designed possible 5-lipoxygenase inhibitor: a-acetoxy-N-[1-(1-(tricyclo[3.3.1.13,7]dec-1-yl)ethyl]benzene acetamide, Acta Cryst., C52, 677-679.
  43. Perrakis, A., Schneider, T. S., Antoniadou-Vyzas, E., Dauter, Z. and Hamodrakas, S. J. (1996) Refinement of 2-amino-6-(4-methyl-1-piperazinyl)-4-tricyclo[3.3.1.13,7]dec-1-yl)-1,3,5-triazine at three different temperatures using image-plate data, J. Appl. Cryst., 29, 261-264.
  44. Agianian, B., Perrakis, A., Kanellopoulos, P. N., Sheldrick B. and Hamodrakas, S. J. (1997) The crystal and molecular structure of p-nitrophenyl-β-D-mannopyranoside ethanol solvate, Acta Cryst., C53, 811-814.
  45. Papadopoulou, P., Galanopoulos, V. K. and Hamodrakas, S. J. (1996) Molecular and supramolecular architecture of the Salmo gairdneri proteinaceous eggshell during development, J. Struct. Biology, 116, 399-412.
  46. Kanellopoulos, P. N., Pavlou, K., Perrakis, A., Agianian, B., Vorgias, C., Mavrommatis, C., Soufi, M., Tucker, P. A. and Hamodrakas, S. J. (1996) The crystal structure of the complexes of Concanavalin A with 4'-nitrophenyl-β-D-mannopyranoside and 4'-nitrophenyl-β-D-glucopyranoside, J. Struct. Biology, 116, 345-355.
  47. Kanellopoulos, P. N., Pavlou, K., Agianian, B., Tucker, P. A. and Hamodrakas, S. J. (1996) A triclinic crystal form of the lectin Concanavalin A, J. Struct. Biol., 117, 16-23.
  48. Hamodrakas, S. J., Kanellopoulos, P. N., Pavlou, K. and Tucker, P. A. (1997) The crystal structure of the complex of Concanavalin A with 4'- methylumbelliferyl-β-D-glucopyranoside, J. Struct. Biol., 118, 23-30.
  49. Benaki, D. C., Aggeli, A., Chryssikos, G. D., Yiannopoulos, Y. D., Brumley, E., Case, S. T., Boden, N. and Hamodrakas, S. J. (1998) Laser-Raman and FT-IR spectroscopic studies of peptide-analogues of silkmoth chorion protein segments, Int. J. Biol. Macromol., 23(1), 49-59.
  50. Pasquier, C. M., Promponas, V. I., Varvayannis, N. J. and Hamodrakas, S. J. (1998) A web server to locate periodicities in a sequence, Bioinformatics, 14(8), 749-50.
  51. Iconomidou, V. A., Willis, J. H. and Hamodrakas, S. J. (1999) Is beta-pleated sheet the molecular conformation which dictates formation of helicoidal cuticle? Insect Biochem. Mol. Biol., 29(3), 285-92.
  52. Promponas, V. J., Palaios, G., Pasquier, C. M., Hamodrakas, J. S. and Hamodrakas S. J. (1999) CoPreTHi: A Web tool which combins transmembrane protein segment prediction methods, In Silico Biology, 3, 1-4.
  53. Pasquier, C., Promponas, V. J., Palaios, G. A., Hamodrakas, J. S., and Hamodrakas, S. J. (1999) A novel method for predicting transmembrane segments in proteins based on a statistical analysis of the SwissProt database: the PRED-TMR algorithm, Protein Eng., 12(5), 381-5.
  54. Pasquier, C., and Hamodrakas, S. J. (1999) An hierarchical artificial neural network system for the classification of transmembrane proteins, Protein Eng., 12(8), 631-4.
  55. Perrakis, A., Antoniadou-Vyzas, E., Tsitsa, P., Lamzin, V. S., Wilson, K. S. and Hamodrakas, S. J. (1999) Molecular, crystal and solution structure of a β-cyclodextrin complex with ADM-10, a potent antimicrobial drug, Carbohydrate Res., 317(1-4), 19-28.
  56. Iconomidou, V. A.; Vriend, G.A. and Hamodrakas, S. J. (2000) Amyloids protect the silkmoth oocyte and embryo, FEBS Letters, 479, 141-5.
  57. Promponas, V. J.; Enright, A. J.; Tsoka, S.; Kreil, D. P.; Leroy, C. and Hamodrakas, S. J.; Sander, C.; Ouzounis, C. A. (2000) CAST: an iterative algorithm for the complexity analysis of sequence tracts. Bioinformatics, 16(10), 915-922.
  58. Iconomidou, V. A., Chryssikos, G. D., Gionis, V., Pavlidis, M. A., Paipetis, A. and Hamodrakas, S. J. (2000) Secondary structure of chorion proteins of the teleostean fish Dentex dentex by ATR FT-IR and FT-Raman spectroscopy, J. Struct. Biol., 132, 112-122.
  59. Iconomidou, V. A., Chryssikos, G. D., Gionis, V., Willis, J. H. and Hamodrakas, S. J. (2001) "Soft"-cuticle protein secondary structure as revealed by FT-Raman, ATR FT-IR and CD spectroscopy, Insect Biochem. Mol. Biol., 31, 877-885.
  60. Liakopoulos, T. D., Pasquier, C. and Hamodrakas, S. J. (2001) A novel tool for the prediction of transmembrane protein topology based on a statistical analysis of the SwissProt database: the OrienTM algorithm, Protein Eng, 14, 387-390.
  61. Karmirantzou, M. and Hamodrakas, S. J. (2001) A database of DNA-binding proteins: an approach for protein family classification, Protein Eng., 14(7), 465-472.
  62. Iconomidou, V. A., Chryssikos, G. D., Gionis, V., Vriend, G., Hoenger, A. and Hamodrakas, S. J. (2001) Amyloid-like fibrils from an 18-residue peptide-analogue of a part of the central domain of the B-family of silkmoth chorion proteins, FEBS Letters, 499, 268-273.
  63. Pasquier, C., Promponas, V. I. and Hamodrakas, S. J. (2001) PRED-CLASS: Cascading neural networks for generalized protein classification and genome-wide applications, Proteins, 44, 361-369.
  64. Iconomidou, V.A. and Hamodrakas, S.J. (2001) Amyloid-like fibrils from a peptide-analogue of the central domain of silkmoth chorion proteins. In A. Aggeli, N. Boden, S, Zhang"Self-Assembling Peptide Systems in Biology, Medicine, and Engineering" , Chapter 12, 161-169, Kluwer Press.
  65. Hamodrakas, S.J., Willis, J.H. and Iconomidou, V.A. (2002) A structural model of the chitin-binding domain of cuticle proteins, Insect Biochem. Mol. Biol., 32,1577-1583.
  66. Papandreou, N. C., Makedonopoulou, S., Antoniadou-Vyza, E. A., Mavridis, I. M. and Hamodrakas, S. J. (2002) 2,4-Diamino-5-(1-naphthyl)-3,5-diaza-1-azoniaspiro[5.5]undeca-1,3-diene chloride, Acta Cryst., C58, 730-732.
  67. Iliopoulos, I., Tsoka, S., Andrade, M., Enright, A.J., Carroll, M., Poullet, P., Promponas, V., Liakopoulos, T., Palaios, G., Pasquier, C., Hamodrakas, S., Tamames, J., Yagnik, A., Tramontano, A., Devos, D., Blaschke, C., Valencia, A., Brett, D., Martin, D., Leroy, C., Rigoutsos, I., Sander, C., Ouzounis, C.A. (2003) Evaluation of Annotation Strategies using an Entire Genome Sequence. Bioinformatics, 19 (6), 717-726.
  68. Iconomidou, V.A., Chryssikos, G.D., Gionis, V., Hoenger, A., Hamodrakas, S.J. (2003) FT-Raman Spectroscopy as diagnostic tool of Congo red binding to amyloids. Biopolymers (Biospectroscopy), 72, 185-192.
  69. Benaki, D.C, Mikros, E., Hamodrakas, S.J. (2003) Conformational Analysis of Peptide Analogues of Silkmoth Chorion Protein Segments Using CD, NMR and Molecular Modelling. Journal of Peptide Science.
  70. Papasaikas, P.K., Bagos, P.G., Litou, Z.I. and Hamodrakas, SJ. (2003) A novel method for GPCR recognition and family classification, from sequence alone, using signatures derived from profile Hidden Markov models, S.A.R-Q.S.A.R Environmen. Research, 14(5-6), 413-420.
  71. Vernikos, G.S., Gkogkas, C.G., Promponas, V.J. and Hamodrakas, S.J. (2003) GeneViTo: visualizing gene-product functional and structural features in genomic datasets, BMC Bioinformatics, 4:53.
  72. Hamodrakas, S.J., Hoenger, A., Iconomidou, V.A. (2004) Amyloid fibrillogenesis of silkmoth chorion protein peptide-analogues via a liquid crystalline intermediate phase. J. Struct. Biol., 145, 226-235.
  73. Pashou, E.E., Litou, Z.I., Liakopoulos, Th.D. and Hamodrakas, S.J. (2004) waveTM: Wavelet-based transmembrane segment prediction. In Silico Biol.4, 0012.
  74. Bagos, P.G., Liakopoulos, T.D., Spyropoulos, I.C., Hamodrakas, S.J. (2004) A Hidden Markov Model capable of predicting and discriminating beta-barrel outer membrane proteins. BMC Bioinformatics, 2004, 5:29.
  75. Bagos, P.G., Liakopoulos, T.D., Spyropoulos, I.C., Hamodrakas, S.J. (2004) PRED-TMBB: A web server for predicting the topology of β-barrel outer membrane proteins Nucleic Acids Res, 32, W400-404.
  76. Bagos, P.G., Liakopoulos, T.D., Hamodrakas, S.J. (2004) Maximum Likelihood and Conditional Maximum Likelihood learning algorithms for Hidden Markov Models with labeled data. Journal of Computational Methods in Sciences and Engineering, In Press.
  77. Papasaikas, P.K., Bagos, P.G., Litou, Z.I., Promponas V.J. and Hamodrakas, S.J. (2004) PRED-GPCR: GPCR recognition and family classification server. Nucleic Acids Res, 32, W380-382.
  78. Spyropoulos, I.C., Liakopoulos, T.D., Bagos, P.G., Hamodrakas, S.J. (2004) TMRPres2D: high quality visual representation of transmembrane protein models. Bioinformatics, 20(17), 3258-3260.
  79. Magkrioti, C.K., Spyropoulos, I.C., Iconomidou, V.A., Willis, Hamodrakas, S.J. (2004) CuticleDB: a relational database of Arthropod cuticular proteins. BMC Bioinformatics, 5: 138.
  80. Elefsinioti, A.L., Bagos, P.G., Spyropoulos, I.C., Hamodrakas, S.J. (2004) A database for G proteins and their interaction with GPCRs. BMC Bioinformatics, 5(1), 208.
  81. Bagos, P.G., Liakopoulos, Hamodrakas, S.J. (2004) Finding beta-barrel outer membrane proteins with a markov chain model. WSEAS Transactions on Biology and Biomedicine, 2(1), 186-189.
  82. Bagos, P.G., Liakopoulos, Hamodrakas, S.J. (2004) Faster Gradient Descent Training of Hidden Markov Models, Using Individual Learning Rate Adaptation. Proceedings of ICGI 2004 Lecture Notes In Artificial Intelligence, 2(1), Vol. 3264, pp. 40-52.
  83. Bagos, P.G., Liakopoulos, T.D., Promponas, V.J., Hamodrakas, S.J. (2004) Topology prediction of β-barrel outer membrane proteins. Proc Indian Natl Sci Acad., B71(1), 19-41.
  84. Bagos, P.G., Liakopoulos, Th.D., Hamodrakas, S.J. (2005) Evaluation of methods for predicting the topology of β-barrel outer membrane proteins and a consensus prediction method. BMC Bioinformatics, 6:7.
  85. Iconomidou, V.A., Willis, J.H., Hamodrakas, S.J. (2005) Unique features of the structural model of hard cuticle proteins: implications for chitin-protein interactions and cross-linking in cuticle. Insect Biochem. Mol. Biol., 35(6), 553-60.
  86. Willis, J.H., Iconomidou, V.A., Smith, R.F. Hamodrakas, S.J. (2005) Cuticular Proteins in 'Comprehensive Insect Science', (L. I. Gilbert, K. Iatrou, and S. Gill, Eds.). Elsevier, Oxford, Vol. 4, Ch. 2, 79-110.
  87. Sgourakis, N.G., Bagos, P.G., Papasaikas, P.K. and Hamodrakas, S.J. (2005) A method for the prediction of GPCRs coupling specificity to G-proteins using refined profile Hidden Markov Models. BMC Bioinformatics, 6:104.
  88. Sgourakis, N.G., Bagos, P.G., Hamodrakas, S.J. (2005) Prediction of the coupling specificity of GPCRs to four families of G-proteins using hidden Markov models and artificial neural networks. Bioinformatics, 21(22), 4101-6.
  89. Bagos, P.G., Liakopoulos, Th.D., Hamodrakas, S.J. (2006) Algorithms for incorporating prior topological information in HMMs: application to transmembrane proteins. BMC Bioinformatics, 7, 189.
  90. Petsalaki, E.I., Bagos, P.G., Litou, Z.I., Hamodrakas, S.J. (2006) PredSL: A Tool for the N-terminal Sequence-based Prediction of Protein Subcellular Localization. Geno. Prot. Bioinfo., 4, 1.
  91. Iconomidou, V.A., Chryssikos, G.D., Gionis V, Galanis, A.S., Cordopatis, P., Hoenger, A., Hamodrakas, S.J. (2006) Amyloid fibril formation propensity is inherent into the hexapeptide tandemly repeating sequence of the central domain of silkmoth chorion proteins of the A-family. J. Struct. Biol., 156, 480-488.
  92. Bagos, P.G., Karnaouri, A.C., Nikolopoulos, G.K., Hamodrakas, S.J. (2007) No evidence for association of CTLA-4 gene polymorphisms with the risk of developing Multiple Sclerosis: a meta-analysis. Multiple Sclerosis. 13, 156-168.
  93. Iconomidou, V.A., Georgaka, M.E., Chryssikos, G.D., Gionis, V., Megalofonou, P., Hamodrakas, S.J. (2007) Dogfish egg case structural studies by ATR FT-IR and FT-Raman spectroscopy. Int. J. Biol. Macromol., 41(1), 102-108.
  94. Hamodrakas, S.J., Christina Liappa, C. Iconomidou, V.A. (2007) Consensus prediction of amyloidogenic determinants in amyloid fibril-forming proteins. Int. J. Biol. Macromol., 41(3),295-300.
  95. Kastritis, P.L., Papandreou, N.C., Hamodrakas, S.J. (2007) Haloadaptation: Insights from comparative modeling studies of halophilic archaeal DHFRs. Int. J.Biol. Macromol., 41(4),447-53.
  96. Karouzou, M.V., Spyropoulos, Y., Iconomidou, V.A., Cornman, R.S., Hamodrakas, S.J., Willis, J.H. (2007) Drosophila cuticular proteins with the R&R Consensus: annotation and classification with a new tool for discriminating RR-1 and RR-2 sequences. Insect Biochem Mol Biol., 37(8), 754-60.
  97. Litou, Z.I., Bagos, P.G., Tsirigos, K.D., Liakopoulos, Th.D., Hamodrakas, S.J. (2008) Prediction of Cell Wall sorting signals in Gram-positive bacteria with a Hidden Markov Model: application to complete genomes. IJBCB, 6(2), 387-401.
  98. Iconomidou, V.A. and Hamodrakas, S.J. (2008) Natural Protective Amyloids. Curr. Prot. Pept. Sci., 9(3), 291-309.
  99. Nikolopoulos, G.K., Dimou, N.L., Hamodrakas, S.J., Bagos, P.G. (2008) Cytokine gene polymorphisms in periodontal disease: a meta-analysis of 53 studies including 4178 cases and 4590 controls. J Clin Periodontol, 35(9), 754-767.
  100. Theodoropoulou, M.C., Bagos, P.G., Spyropoulos, I.C., Hamodrakas, S.J. (2008) gpDB: a database of GPCRs, G-proteins, effectors and their interactions. Bioinformatics, 24(12), 1471-1472.
  101. Bagos, P.G., Tsirigos, K.D., Liakopoulos, T.D., Hamodrakas, S.J. (2008) Prediction of Lipoprotein Signal Peptides in Gram-Positive Bacteria with a Hidden Markov Model. J Proteome Res, 7(12), 5082-5093.
  102. Skopeliti, M., Iconomidou, V.A., Derhovanessian, E., Pawelec, G., Voelter, W., Kalbacher, H., Hamodrakas, S.J., Tsitsilonis, O.E. (2009) Prothymosin alpha immunoactive carboxyl-terminal peptide TKKQKTDEDD stimulates lymphocyte reactions, induces dendritic cell maturation and adopts a beta-sheet conformation in a sequence-specific manner. Mol Immunol, 46(5), 784-792.
  103. Bagos, P.G., Tsirigos, K.D. Plessas, S.K., Liakopoulos, T.D., Hamodrakas, S.J . (2009) Prediction of signal peptides in archaea. Protein Eng Des Sel, 22(1), 27-35.
  104. Frousios, K.K., Iconomidou, V.A., Karletidi, C.M., Hamodrakas, S.J. (2009) Amyloidogenic determinants are usually not buried. BMC Struct Biol., 9(1), 44.
  105. Bagos, P.G., Tsaousis, G.N., Hamodrakas, S.J.(2009) How many 3D structures do we need to train a predictor? Genomics Proteomics Bioinformatics, 7(3):128-37.
  106. Dimou, N.L., Nikolopoulos, G.K., Hamodrakas, S.J., Bagos, P.G.(2010) Fcgamma receptor polymorphisms and their association with periodontal disease: a meta-analysis. J Clin Periodontol.,37(3):255-65.
  107. Anthopoulos, P.G., Hamodrakas, S.J., Bagos, P.G. (2010) Apolipoprotein E polymorphisms and type 2 diabetes: a meta-analysis of 30 studies including 5423 cases and 8197 controls. Mol Genet Metab., 100(3):283-91.
  108. Tsaousis, G.N., Tsirigos, K.D., Andrianou, X.D., Liakopoulos, T.D., Bagos, P.G., Hamodrakas, S.J. (2010) ExTopoDB: A database of experimentally derived topological models of transmembrane proteins. Bioinformatics, 26(19): 2490?2492.
  109. Satagopam, V.P., Theodoropoulou, M.C., Stampolakis, C.K., Pavlopoulos, G.A., Papandreou, N.C., Bagos, P.G., Schneider, R., Hamodrakas, S.J.(2010) GPCRs, G-proteins, Effectors and their interactions: Human-gpDB, a database employing advanced visualization tools and data integration techniques. Database (Oxford), Vol. 2010, Article ID baq019.
  110. Papandreou, N.C., Iconomidou, V.A., Willis, J.H., Hamodrakas, S.J. (2010) A possible structural model of members of the CPF family of cuticular proteins implicating binding to components other than chitin. J Insect Physiol., 56(10), 1420-1426.
  111. Tsirigos, K.D., Bagos, P.G., Hamodrakas, S.J. (2011) OMPdb: A database of â-barrel outer membrane proteins from Gram negative bacteria. Nucleic Acids Res., 39(Database issue): D324-31. [Epub ahead of print].
  112. Hamodrakas, S.J. (2011) Protein aggregation and amyloid fibril formation prediction software from primary sequence: towards controlling the formation of bacterial inclusion bodies. FEBS J., [Epub ahead of print], doi: 10.1111/j.1742-4658.2011.08164.x.
  113. Srivastava, A.K., Iconomidou, V.A., Chryssikos, G.D., Gionis, V., Kumar, K., Hamodrakas, S.J. (2011) Secondary structure of chorion proteins of the Lepidoptera Pericallia ricini and Ariadne merione by ATR FT-IR and micro-Raman spectroscopy. Int J Biol Macromol.,[Epub ahead of print].
  114. Iconomidou, V.A., Cordopatis, P., Hoenger, A., Hamodrakas, S.J. (2011) The silkmoth eggshell as a natural amyloid shield for the safe development of insect oocyte and embryo: Insights from studies of silkmoth chorion protein peptide-analogues of the B family. Peptide Science,Biopolymers 96, [Epub ahead of print], doi: 10.1002/bip.21606