2017 2016 2015 2014 2013 2012 2011 2010 2009 2008 2007 2006 2005 2004 2003 2002 2001 2000 1999 1998 1997 1996 1995 1993 1992 1991 1989 1988 1987 1986 1985 1984 1983 1982 1978 1977 1974
In Press
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Tsiolaki P.L, Nastou K.C., Hamodrakas S.J., Iconomidou V.A. (2017) Mining databases for protein aggregation: a review. Amyloid (In Press) [Epub ahead of print] [Abstract] [PDF] doi: 10.1080/13506129.2017.1353966
Tsiolaki, P.L., Nastou K.C., Louros N.N., Hamodrakas S.J., Iconomidou V.A. (2017) Exploring the amyloidogenicity of Clusterin: a structural and bioinformatics analysis. Advances in Experimental Medicine and Biology (In Press) [Abstract] [PDF]
2017
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Louros N.N., Tsiolaki P.L, Baltoumas F.A., Chryssikos G.D., Gionis V., Hamodrakas S.J., Iconomidou V.A. (2017) Tracking the amyloidogenic core of IAPP amyloid fibrils: Insights from micro-Raman spectroscopy. J. Struct. Biol. Aug;199(2):140-152 [Epub ahead of print] [Abstract] [PDF] doi: 10.1016/j.jsb.2017.06.002.
Biza, K.V.*, Nastou, K.C.*, Tsiolaki, P.L.*, Mastrokalou, C.V., Hamodrakas, S.J., Iconomidou, V.A. (2017) The amyloid interactome: Exploring protein aggregation. PLoS ONE Mar 1;12(3):e0173163. [Abstract] [PDF] (*: Equally contributing authors) doi:10.1371/journal.pone.0173163.
Tsaousis, G.N., Theodoropoulou, M.C., Hamodrakas, S.J., Bagos, P.G. (2017) Predicting Alpha Helical Transmembrane Proteins Using HMMs. Methods Mol. Biol. 1552:63-82 [Abstract] [Full Text] doi:10.1007/978-1-4939-6753-7_5.
Tsaousis, G.N., Hamodrakas, S.J., Bagos, P.G. (2017) Predicting Beta Barrel Transmembrane Proteins Using HMMs. Methods Mol. Biol. 1552:43-61 [Abstract] [Full Text] doi:10.1007/978-1-4939-6753-7_4.
2016
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Kanost, M.R., (...), Hamodrakas, S.J., (...), Blissard (2016) Multifaceted biological insights from a draft genome sequence of the tobacco hornworm moth, Manduca sexta. Insect Bioch. and Mol. Biol. 76 (2016) pp. 118-147. [Abstract] [PDF] doi: 10.1002/bip.22882.
Tsiolaki, P.L., Louros, N.N., Zompra, A.A.,Hamodrakas, S.J., Iconomidou, V.A. (2016) Unraveling t he aggregation propensity of human insulin C-peptide. Biopolymers. 2016 Jun 3. [Epub ahead of print] [Abstract] [PDF] doi: 10.10 16/j.ibmb.2016.07.005.
Louros, N.N., Bolas, G.M., Tsiolaki, P.L., Hamodrakas, S.J., Iconomidou, V.A. (2016) Intrinsic Aggregation Propensity of the CsgB Nucleator Protein is Crucial for Curli Fiber Formation. J. Struct. Biol. Aug;195(2):179-89. Epub 2016 May 28. [Abstract] [PDF] doi: 10.1016/j.jsb.2016.05.012.
Baltoumas, F.A., Theodoropoulou, M.C., Hamodrakas, S.J. (2016) Molecular dynamics simulations and structure-based network analysis reveal structural and functional aspects of G-protein coupled receptor dimer interactions. J. Comput. Aided. Mol. Des. Jun;30(6):489-512. [Abstract] [PDF] doi: 10.1007/s10822-016-9919-y.
Nastou, K.C., Tsaousis, G.N., Papandreou, N.C., Hamodrakas, S.J. (2016) MBPpred: Proteome-wide detection of membrane lipid-binding proteins using profile Hidden Markov Models. Biochim. Biophys. Acta Volume 1864, Issue 7, pp. 747–754. [Abstract] [PDF] [Supplementary Material] doi: 10.1016/j.bbapap.2016.03.015.
Louros, N.N., Baltoumas, F.A., Hamodrakas, S.J., Iconomidou, V.A. (2016) A β-solenoid model of the Pmel17 repeat domain: insights to the formation of functional amyloid fibrils. J. Comput. Aided. Mol. Des. Feb;30(2):153-64. [Abstract] [PDF] doi: 10.1007/s10822-015-9892-x.
Louros, N.N., Chrysina, E.D., Baltatzis, G.E., Patsouris, E.S., Hamodrakas, S.J., Iconomidou, V.A. (2016) A common "aggregation-prone" interface possibly participates in the self-assembly of human zona pellucida proteins. FEBS Letters, 590: 619–630. [Abstract] [PDF]doi: 10.1002/1873-3468.12099.
Kostiou V.D., Theodoropoulou M.C., Hamodrakas S.J. (2016) GprotPRED: Annotation of Gα, Gβ and Gγ subunits of G-proteins using profile hidden Markov models (pHMMs) and application to proteomes.Biochim. Biophys. Acta Volume 1864, Issue 5, pp. 435–440 [Abstract] [PDF]doi: 10.1016/j.bbapap.2016.02.005.
Louros, N.N., Iconomidou, V.A. (2016) Identification of an amyloid fibril forming segment of human Pmel17 repeat domain (RPT domain). Biopolymers. 2016 Jan;106(1):133-9. [Abstract] [PDF] doi: 10.1002/bip.22746.
Rerra, A.I.G., Grimanelli, V.P., Papandreou, N.C., Hamodrakas, S.J. (2016) Optimizing the Aggregation Propensity of Therapeutic Monoclonal Antibodies against Cancer and Autoimmune Diseases: A Computational Study. Int. J. Biochem. Res. Rev. 10(1): 1-15, 2016, Article no.IJBcRR.23216 [Abstract] [PDF] doi: 10.9734/IJBCRR/2016/23216
2015
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Tsiolaki, P.L., Louros, N.N., Hamodrakas, S.J., Iconomidou, V.A. (2015) Exploring the 'aggregation-prone' core of human Cystatin C: A structural study. J. Struct. Biol. Sep;191(3):272-80. Epub 2015 Jul 31. [Abstract] [PDF] doi: 10.1016/j.jsb.2015.07.013
Louros, N.N., Tsiolaki, P.L., Griffin, M.D., Howlett, G.J., Hamodrakas, S.J., Iconomidou, V.A. (2015) Chameleon ‘aggregation-prone’ segments of apoA-I: A model of amyloid fibrils formed in apoA-I amyloidosis. Int. J. Biol. Macromol. Volume 79, pp. 711-718, August 2015. [Abstract] [PDF] doi: 10.1016/j.ijbiomac.2015.05.032
Louros, N.N., Tsiolaki, P.L., Zompra, A.A., Pappa, E.V., Magafa, V., Pairas, G., Cordopatis, P., Cheimonidou, C., Trougakos, I.P., Iconomidou, V.A., Hamodrakas, S.J.(2015) Structural Studies and Cytotoxicity Assays of "Aggregation-Prone" IAPP8-16 and its Non-Amyloidogenic Variants Suggest its Important Role in Fibrillogenesis and Cytotoxicity of Human Amylin (hIAPP). Biopolymers Volume 104, Issue 3, pp. 196–205, May 2015. [Abstract] [PDF] doi: 10.1002/bip.22650
Papadimitriou, K., Anastasiou, R., Maistrou, E., Plakas, T., Papandreou, N.C., Hamodrakas, S.J., Ferreira, S., Supply, P., Renault, P., Pot, B., Tsakalidou, E.(2015) Acquisition through horizontal gene transfer of plasmid pSMA198 by Streptococcus macedonicus ACA-DC 198 points towards the dairy origin of the species. PLoS One. 2015 Jan 13;10(1):e0116337. [Abstract] [PDF] doi: 10.1371/journal.pone.0116337
Tsiolaki, P.L., Hamodrakas, S.J., Iconomidou, V.A. (2015) The pentapeptide LQVVR plays a pivotal role in human cystatin C fibrillization. FEBS Lett. 2015 Jan 2;589(1):159-64. Epub 2014 Dec 3. [Abstract] [PDF] doi: 10.1016/j.febslet.2014.11.041
2014
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Louros, N.N., Petronikolou N., Karamanos T., Cordopatis P., Iconomidou, V.A., Hamodrakas, S.J. (2014) Structural studies of 'aggregation-prone' peptide-analogues of teleostean egg chorion ZPB proteins. Biopolymers [Abstract] [PDF] doi: 110.1002/bip.22563
Ioannidou, Z.S., Theodoropoulou, M.C., Papandreou, N.C., Willis, J.H., Hamodrakas, S.J. (2014) CutProtFam-Pred: Detection and classification of putative structural cuticular proteins from sequence alone, based on profile Hidden Markov Models. Insect. Biochem. Mol. Biol., Volume 52, September 2014, Pages 51-59. [Abstract] [Full Text] doi: 10.1016/j.ibmb.2014.06.004
Nastou, K.C., Tsaousis, G.N., Kremizas, K.E., Litou, Z.I., Hamodrakas, S.J. (2014) The Human Plasma Membrane Peripherome: Visualization and Analysis of Interactions. BioMed Research International, vol. 2014. [Abstract] [PDF] doi: 10.1155/2014/397145
Papadimitriou, K., Anastasiou, R., Mavrogonatou, E., Blom, J., Papandreou, N.C., Hamodrakas, S.J., Ferreira, S., Renault, P., Supply, P., Pot, B., Tsakalidou, E. (2014) Comparative genomics of the dairy isolate Streptococcus macedonicus ACA-DC 198 against related members of the Streptococcus bovis/Streptococcus equinus complex. BMC Genomics, 15:272. [Abstract] [PDF] doi: 10.1186/1471-2164-15-272
Tsaousis, G.N., Bagos, P.G., Hamodrakas, S.J. (2014) HMMpTM: Improving transmembrane protein topology prediction using phosphorylation and glycosylation site prediction. Biochim Biophys Acta., 1844(2): 316-322. [Abstract] [PDF] doi: 10.1016/j.bbapap.2013.11.001
Louros, N.N., Iconomidou, V.A., Tsiolaki, P.L., Chrysina, E.D., Baltatzis, G.E., Patsouris, E.S., Hamodrakas, S.J.(2014) An N-terminal pro-atrial natriuretic peptide (NT-proANP) 'aggregation-prone' segment involved in isolated atrial amyloidosis. FEBS Lett., 588: 52-57. [Abstract] [PDF] doi: 10.1016/j.febslet.2013.10.049
2013
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Louros, N.N., Iconomidou, V.A., Giannelou, P., Hamodrakas, S.J. (2013) Structural Analysis of Peptide-Analogues of Human Zona Pellucida ZP1 Protein with Amyloidogenic Properties: Insights into Mammalian Zona Pellucida Formation. PLoS ONE 8(9): e73258. [Abstract] [PDF] doi: 10.1371/journal.pone.0073258
Gypas, F., Tsaousis, G.N., Hamodrakas, S.J. (2013) mpMoRFsDB: a database of molecular recognition features in membrane proteins. Bioinformatics, 29(19):2517-8. [Abstract] [PDF] doi: 10.1093/bioinformatics/btt427
Baltoumas, F.A., Theodoropoulou, M.C., Hamodrakas, S.J. (2013) Interactions of the α-subunits of heterotrimeric G-proteins with GPCRs, effectors and RGS proteins: A critical review and analysis of interacting surfaces, conformational shifts, structural diversity and electrostatic potentials. J Struct Biol., 182(3): 209-18. [Abstract] [PDF] [Supplementary material] doi: 10.1016/j.jsb.2013.03.004.
Iconomidou, V.A., Leontis, A., Hoenger, A., Hamodrakas, S.J. (2013) Identification of a novel 'aggregation-prone'/'amyloidogenic determinant' peptide in the sequence of the highly amyloidogenic human calcitonin. FEBS Lett., 587: 569-574. [Abstract] [PDF] doi: 10.1016/j.febslet.2013.01.031.
Kotta-Loizou, I., Tsaousis, G.N., Hamodrakas, S.J. (2013) Analysis of Molecular Recognition Features (MoRFs) in membrane proteins. Biochim Biophys Acta., 1834(4): 798-807. [Abstract] [PDF] doi: 10.1016/j.bbapap.2013.01.006.
Giannopoulos, N.G., Michalopoulos, I., Papandreou, N.C., Malatras, A., Iconomidou, V.A., Hamodrakas, S.J. (2013) LepChorionDB, a database of Lepidopteran chorion proteins and a set of tools useful for the identification of chorion proteins in Lepidopteran proteomes. Insect Biochem Mol Biol. , 43: 189-196. [Abstract] [PDF] doi: 10.1016/j.ibmb.2012.12.001.
Tsolis, A.C., Papandreou, N.C., Iconomidou, V.A., Hamodrakas, S.J. (2013) A Consensus Method for the Prediction of "Aggregation-Prone" Peptides in Globular Proteins. PLoS ONE, 8(1): e54175. [Abstract] [PDF] doi:10.1371/journal.pone.0054175
2012
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Willis, J.H., Papandreou, N.C., Iconomidou, V.A., Hamodrakas, S.J. (2012) Cuticular proteins. Chapter 5 in Insect Molecular Biology and Biochemistry (ed. L. I. Gilbert) Academic Press pp. 134-166. [PDF] ISBN: 9780123847478
Stoubos, S., Anthopoulos, P.G., Hamodrakas, S.J., Bagos, P.G. (2012) The association between apolipoprotein E gene polymorphisms and essential hypertension: a meta-analysis of 45 studies including 13940 cases and 16364 controls. Journal of Human Hypertension. [Abstract] [PDF]doi: 10.1038/jhh.2012.37
Spyridopoulou, K., Dimou, N.L., Hamodrakas, S.J., Bagos, P.G. (2012) Methylene Tetrahydrofolate Reductase gene polymorphisms and their association with methotrexate toxicity: A meta-analysis. Pharmacogenetics and Genomics, 22(2): 117-33. [Abstract] [PDF] doi: 10.1097/FPC.0b013e32834ded2a
Iconomidou, V.A., Pheida, D., Hamodraka, E.S., Antony, C., Hoenger, A., Hamodrakas, S.J. (2012) An amyloidogenic determinant in N-terminal pro-brain natriuretic peptide (NT-proBNP): Implications for cardiac amyloidoses. Biopolymers: Peptide Science, 98(1): 67-75.[Abstract] [PDF] doi: 10.1002/bip.21698.
2011
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Chatzigeorgiou, K.S., Sergentanis, T.N., Tsiodras, S., Hamodrakas, S.J., Bagos, P.G. (2011) Phoenix 100 versus Vitek 2 in the Identification of Gram-Positive and Gram-Negative Bacteria: a Comprehensive Meta-Analysis. J Clin Microbiol., 49(9): 3284-91.[Abstract] [PDF] doi:10.1128/JCM.00182-11
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., 278(14): 2428-2435. [Abstract] [PDF] doi: 10.1111/j.1742-4658.2011.08164.x.
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(6): 723–733. [Abstract] [PDF] doi: 10.1002/bip.21606
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, 49(3): 317-22. [Abstract] [PDF] doi: 10.1016/j.ijbiomac.2011.05.006
Tsirigos, K.D., Bagos, P.G. and Hamodrakas, S.J. (2011) OMPdb: A database of ß-barrel outer membrane proteins from Gram negative bacteria. Nucleic Acids Res., 39(Database issue): D324-31. [Abstract] [PDF]
2010
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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. [Abstract] [PDF]
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. [Abstract] [PDF]
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. [Abstract] [PDF]
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. [Abstract] [PDF]
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.[Abstract] [PDF]
2009
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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. [Abstract] [PDF]
Frousios, K.K., Iconomidou, V.A., Karletidi, C.M. and Hamodrakas, S.J. (2009) Amyloidogenic determinants are usually not buried. BMC Struct Biol. 9(1): 44. [Abstract] [PDF]
Bagos, P.G., Tsirigos, K.D., Plessas, S.K., Liakopoulos, T.D. and Hamodrakas, S.J. (2009) Prediction of signal peptides in archaea. Protein Eng Des Sel , 22: 27-35. [Abstract] [PDF]
Skopeliti, M., Iconomidou, V.A., Derhovanessian, E., Pawelec, G., Voelter, W., Kalbacher, H., Hamodrakas, S.J. and 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. [Abstract] [PDF]
2008
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Bagos, P.G., Tsirigos, K.D., Liakopoulos, T.D. and Hamodrakas, S.T. (2008) Prediction of Lipoprotein Signal Peptides in Gram-Positive Bacteria with a Hidden Markov Model. J Proteome Res. 7(12): 5082-5093 [Abstract] [PDF]
Nikolopoulos, G.K., Dimou, N.L., Hamodrakas, S.J. and 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: 754-767. [Abstract] [PDF]
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):1471-2. [Abstract] [PDF]
Iconomidou, V.A. and Hamodrakas, S.J. (2008) Natural Protective Amyloids. Curr. Prot. Pept. Sci. 9(3): 291-309. [Abstract]
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. JBCB , 6(2):387-401. [Abstract] [PDF]
2007
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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. [Abstract] [PDF]
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. [Abstract] [PDF]
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. [Abstract] [PDF]
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. [Abstract] [PDF]
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. [Abstract] [PDF]
2006
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Ahram M, Litou ZI, Fang R, Al-Tawallbeh G. (2006) Estimation of membrane proteins in the human proteome. In Silico Biol. , 6(5): 379-86. [Abstract] [HTML]
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. [Abstract] [PDF]
Bagos, P.G., Liakopoulos, Th.D. and Hamodrakas, S.J. (2006) Algorithms for incorporating prior topological information in HMMs: application to transmembrane proteins. BMC Bioinformatics, 7: 189. [Abstract] [PDF]
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): 48-55. [Abstract] [PDF]
2005
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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. [Abstract] [PDF]
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. [Abstract] [PDF]
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. [PDF]
Bagos, P.G., Liakopoulos, Th.D. and 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. [Abstract] [PDF]
Iconomidou, V.A., Willis, J.H. and 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. [Abstract] [PDF]
Bagos, P.G., Liakopoulos, T.D., Promponas, V.J., Hamodrakas, S.J. (2005) Topology prediction of β-barrel outer membrane proteins.Proc Indian Natl Sci Acad, B71(1): 19-41. [PDF]
2004
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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. [Abstract] [PDF]
Spyropoulos, I.C., Liakopoulos, T.D., Bagos, P.G. and Hamodrakas, S.J. (2004) TMRPres2D: high quality visual representation of transmembrane protein models. Bioinformatics, [Epub ahead of print] [Abstract] [PDF]
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. [Abstract] [PDF]
Bagos, P.G., Liakopoulos, T.D., Spyropoulos, I.C. and 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. [Abstract] [PDF]
Bagos P.G., Liakopoulos T.D. and 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]
Bagos P.G., Liakopoulos T.D., Spyropoulos I.C. and Hamodrakas S.J. (2004) A Hidden Markov Model capable of predicting and discriminating β-barrel outer membrane proteins. BMC Bioinformatics, 2004, 5:29. [Abstract] [PDF]
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. [HTML]
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, 226-35. [Abstract] [PDF]
Magkrioti CK, Spyropoulos IC, Iconomidou VA, Willis JH, Hamodrakas SJ. (2004) cuticleDB: a relational database of Arthropod cuticular proteins. BMC Bioinformatics. 5(1):138. [Abstract] [PDF]
Bagos, P.G., Liakopoulos, T.D., 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. [PDF]
Bagos P.G., Liakopoulos Th.D. and 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 Vol. 3264, pp. 40-52. [PDF]
2003
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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 [Abstract] [PDF]
Papasaikas P.K., Bagos P.G., Litou Z.I, Hamodrakas S.J. (2003) A novel method for GPCR recognition and family classification from sequence alone using signatures derived from profile hidden Markov models. SAR QSAR Environ Res., 14, 413-20. [Abstract] [PDF]
Vernikos G.S., Gkogkas C.G., Promponas V.J., Hamodrakas S.J. (2003) GeneViTo: Visualizing gene-product functional and structural features in genomic datasets. BMC Bioinformatics, 4, 53 [Abstract] [PDF]
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 [Abstract] [PDF]
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. [Abstract] [PDF]
2002
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Hamodrakas S.J., Willis J.H., Iconomidou V.A. (2002) A structural model of the chitin-binding domain of cuticle proteins, Insect Biochem Mol Biol, 32, 1577-1583. [Abstract] [PDF]
Papandreou N.C., Makedonopoulou S., Antoniadou-Vyza E.A., Mavridis I.M., Hamodrakas S.J. (2002) 2,4-Diamino-5-(1-naphthyl)-3,5-diaza-1-azoniaspiro[5.5]undeca-1,3-diene chloride. Acta Crystallogr C. , 58, 730-732. [Abstract] [PDF]
2001
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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. [Abstract] [PDF]
Liakopoulos, T. D., Pasquier, C., 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. [Abstract] [PDF]
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. [Abstract] [PDF]
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. [Abstract] [PDF]
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. [Abstract] [PDF]
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.[PDF]
2000
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Iconomidou, V. A.; Vriend, G.A. and Hamodrakas, S. J. (2000) Amyloids protect the silkmoth oocyte and embryo, FEBS Letters, 479, 141-5. [Abstract] [PDF]
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. [Abstract] [PDF]
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. [Abstract] [PDF]
1999
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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. [Abstract] [PDF]
Promponas, V. J., Palaios, G., Pasquier, C. M., Hamodrakas, J. S. and Hamodrakas S. J. (1999) CoPreTHi: A Web tool which combines transmembrane protein segment prediction methods, In Silico Biology, 3, 1-4. [Abstract]
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. [Abstract] [PDF]
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. [Abstract] [PDF]
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. [Abstract] [PDF]
1998
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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. [Abstract] [PDF]
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. [Abstract] [PDF]
1997
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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-α-D-glucopyranoside, J. Struct. Biol., 118, 23-30. [Abstract] [PDF]
Agianian, B., Perrakis, A., Kanellopoulos, P. N., Sheldrick B. and Hamodrakas, S. J. (1997) The crystal and molecular structure of p-nitrophenyl-α-D-mannopyranoside ethanol solvate, Acta Cryst., C53, 811-814. [PDF]
1996
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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. [Abstract] [PDF]
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-α-D-mannopyranoside and 4'-nitrophenyl-α-D-glucopyranoside, J. Struct. Biology, 116, 345-355. [Abstract] [PDF]
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. [Abstract] [PDF]
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. [PDF]
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. [PDF]
1995
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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. [Abstract] [PDF]
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. [Abstract] [PDF]
1993
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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-α-D-glucopyranoside, Acta Cryst., C49, 298-300. [PDF]
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 γ-lactam ketone and its Mannich base, J. Cryst. Spectrosc. Res., 23, 663-668. [PDF]
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. [PDF]
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. [PDF]
1992
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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. [PDF]
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. [Abstract] [PDF]
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. [PDF]
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. [PDF]
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). [Abstract][PDF]
1991
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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. [PDF]
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. [Abstract] [PDF]
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. [Abstract] [PDF]
1989
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Hamodrakas, S. J., Alexandraki, E., Troganis, A. and Stassinopoulou, C.I. (1989) Models of binding of 4'-nitrophenyl α-D-mannopyranoside to the lectin concanavalin A, Int. J. Biol. Macromol., 11 (1), 17-22. [Abstract] [PDF]
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.[Abstract] [PDF]
1988
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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. [Abstract][PDF]
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. [Abstract][PDF]
1987
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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. [Abstract] [PDF]
1986
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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. [PDF]
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. [PDF]
1985
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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. [Abstract] [PDF]
1984
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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. [Abstract]
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. [PDF]
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. [Abstract] [PDF]
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. [PDF]
1983
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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. [Abstract] [PDF]
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. [PDF]
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. [PDF]
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. [PDF]
1982
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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. [PDF]
Hamodrakas, S. J., Jones, C. W. and Kafatos, F. C. (1982) Secondary structure predictions for silkmoth chorion proteins, Biochim. Biophys. Acta, 700, 42-51. [PDF]
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. [PDF]
1978
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Hamodrakas, S. J., Akrigg, D. and Sheldrick, B. (1978) (The crystal structure of) Methyl dehydroabietate, C21H30O2, Cryst. Struct. Comm., 7, 429.
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. [PDF]
1977
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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.
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.
1974
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Hamodrakas, S. J., Geddes, A. J. and Sheldrick, B. (1974) X-ray analysis of disodium cromoglycate, Journal of Pharmacy and Pharmacology, 26, 54.[PDF]
Hamodrakas, S. J., Geddes, A. J. and Sheldrick, B. (1974) The crystal structure of β-methylphenylcholine ether bromide, Acta Cryst., B30, 881. [PDF]
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.
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).