Active members
Other than NMG, the group presently comprises Ignatiadou Danai (Computational analysis and modeling of the interaction between the FERRY complex and nucleic acids, BSc), Latsiou Antigone (Application of UMAP dimensionality reduction to folding molecular dynamics simulations, BSc).
PhD theses
- Lesgidou, N.L. (2023) "Structure and Dynamics Studies of Disease-Related Proteins through Molecular Dynamics Simulations", PhD thesis (PDF 5.6 MBytes).
- Apostolou-Karampelis, K. (2016) "Study of compositional patterns, distributions and symmetries of nucleotide motifs at genome scale", PhD thesis (PDF 8.3 MBytes).
- Georgoulia P. (2012) "Computational studies of foldable tetra- and penta-peptides", PhD thesis (PDF 10 MBytes).
MSc theses
- Melas A. (2026) "Automating the multidimensional clustering of data derived from a Principal Component Analysis of molecular dynamics trajectories using HDBSCAN", MSc thesis (PDF 1.9 MBytes), Presentation (PDF 4.8 MBytes).
- Panagopoulos E.-M. (2024) "Modeling the interaction between a non-specific DNA-binding peptide and canonical B-DNA", MSc thesis (PDF 1.1 MBytes), Presentation (PDF 1.8 MBytes).
- Tafanidis A. (2024) "Using AlphaFold2 to predict structures of non-naturally occurring proteins: the ROP case", MSc thesis (PDF 3.2 MBytes), Presentation (PDF 2.3 MBytes).
- Mitraina G. (2023) "Structural computational biology studies of an antimicrobial peptide with a WWW motif", MSc thesis (PDF 1.8 MBytes), Presentation (PDF 1.8 MBytes).
- Alexiadou D. (2022) "Structural computational biology studies of a non-specific DNA-binding peptide", MSc thesis (PDF 1.7 MBytes).
- Chatzidimitriou D. (2015) "Approaching the phase problem of X-Ray crystallography with feed forward neural networks", MSc thesis (PDF 3.0 MBytes).
BSc theses
- Zachariadis, A. (2026) "In silico folding of a three-stranded β-sheet peptide with aromatic cross-links", Diploma thesis (PDF 4.1 MBytes).
- Tsevis, A. (2026) "NOEmd : a computer program to automate the comparison between experimental NMR data and molecular dynamics simulations", Diploma thesis (PDF 1.7 MBytes).
- Svingou, N. (2026) "The Repressor of Primer protein : to be native-like, or not to be ? Comparative computational studies of the D30P vs A31P mutants", Diploma thesis (PDF 2.1 MBytes).
- Tsabazi, V. (2026) "A memory-efficient method for quantifying convergence of molecular dynamics trajectories", Diploma thesis (PDF 3.9 MBytes).
- Prigkou, I. (2025) "Quantifying the effect of mutations on protein stability using molecular dynamics simulations : the case of the D30G ROP mutant", Diploma thesis (PDF 4.1 MBytes).
- Karapostoli, G. (2025) "How protein turns unfold : molecular dynamics simulations of a ROP protein variant carrying a partially unfolded turn", Diploma thesis (PDF 2.4 MBytes).
- Papoutsis, N. (2025) "Mapping the folding landscape of a peptide that lacks secondary structure elements: the EPI-X4 case", Diploma thesis (PDF 1.8 MBytes).
- Touliopoulos, S. (2024) "Atomic density distributions in proteins : structural and functional implications", Diploma thesis (PDF 1.5 MBytes).
- Zigkou, A.-M. (2023) "Folding of the human Pin1 WW domain using molecular dynamics simulations", Diploma thesis (PDF 3.1 MBytes).
- Mantis, C. (2023) "PCA-based clustering of protein structures", Diploma thesis (PDF 1.0 MBytes).
- Nikolopoulou, D. (2022) "Homology modeling of the complex between the Repressor of Primer protein and its cognate RNA kissing complex", Diploma thesis (PDF 1.8 MBytes).
- Vouzina, O.-D. (2022) "Folding studies of the A31P Rop mutant using molecular dynamics simulations", Diploma thesis (PDF 2.9 MBytes).
- Kolypetris, G. (2022) "Conserved clusters of contacts in protein structures", Diploma thesis (PDF 1.1 MBytes).
- Chatzopoulou, M. (2022) "Structural modeling of rRM6, a reversed sequence protein", Diploma thesis (PDF 2.7 MBytes).
- Giannaki, A.-A. (2021) "Buried β-turns in hydrophobic cores: Structural and Functional Implications", Diploma thesis (PDF 3.6 MBytes).
- Gkogka, I. (2021) "Folding dynamics of the T-peptide in DMSO", Diploma thesis (PDF 3.4 MBytes).
- Athanasopoulos, P. (2020) "Crystallographic studies of a DNA methyltransferase", Diploma thesis (PDF 6.3 MBytes).
- Efraimidis E.-O. (2020) "Folding of VG16KRKP, an antimicrobial peptide", Diploma thesis (PDF 2.0 MBytes).
- Valaroutsou E. (2019) "Molecular dynamics simulation of a Vammin-derived mutant peptide", Diploma thesis (PDF 1.9 MBytes).
- Arvaniti K.-O. (2019) "Peptide folding in TFE/water mixtures", Diploma thesis (PDF 2.9 MBytes).
- Kaymaz B. (2019) "Validation of the AMBER 15SB force field using an α-Lactalbumin-derived peptide", Erasmus+ Diploma thesis (PDF 1.8 MBytes).
- Mitsikas D. (2018) "Propensities of Asn-Gly containing heptapeptides to form β-turn structures : A Molecular Dynamics simulation approach", Diploma thesis (PDF 4.2 MBytes).
- Boukoura T. (2018) "In silico mutagenesis and docking studies of an influenza hemagglutinin/receptor complex", Diploma thesis (PDF 8.5 MBytes).
- Chatzisavvas A. (2018) "Transition state identification via Q-T diagrams : application to the CLN025 peptide", Diploma thesis (PDF 2.1 MBytes).
- Chatzistylianou P. (2017) "Folding of an amyloid Αβ-derived peptide", Diploma thesis (PDF 1.5 MBytes).
- Adamidou T. (2017) "Folding of an FTZ-derived peptide", Diploma thesis (PDF 1.0 MBytes).
- Moschou D. (2017) "Application of Artificial Neural Networks to the crystallographic phase problem", Diploma thesis (PDF 1.7 MBytes).
- Riziotis I. (2017) "Two residue periodicities in protein structures: Results from a systematic search in 4-dimensional Ramachandran space", Diploma thesis (PDF 4.0 MBytes).
- Serafeim A.-P. (2016) "Assessing the accuracy of the AMBER family of force fields : the CLN025 peptide", Diploma thesis (PDF 2.5 MBytes).
- Baltzis A. (2015) "Accuracy of folding simulations for marginally stable peptides : the HP21 case", Diploma thesis (PDF 2.8 MBytes).
- Koumoundourou E.-A. (2015) "Folding molecular dynamics simulations of a FMRF-amide-like peptide from C. elegans", Diploma thesis (PDF 2.3 MBytes).
- Tafarli T. (2014) "Folding molecular dynamics simulations of ubiquitin's N-terminal peptide", Diploma thesis (PDF 4.6 MBytes).
- Koukos P.I. (2013) "grcarma: A Fully Automated Task-Oriented Interface for the Analysis of Molecular Dynamics Trajectories", Diploma thesis (PDF 2.9 MBytes).
- Patmanidis I. (2013) "Folding simulations of the choline-binding repeat from the protein LytA", Diploma thesis (PDF 3.9 MBytes).
- Kontopoulos D.-G. (2012) "Pinda : a gene duplication detection program", Diploma thesis (PDF 1.7 MBytes).
- Kousa A. (2011) "Sequence-similar, structure dissimilar proteins: Anfinsen revisited.", Diploma thesis (PDF 4.7 MBytes).
- Patapati K. K. (2010) "Molecular dynamics simulations of the αLa(101-111) peptide of α-Lactalbumin", Diploma thesis (PDF 4.6 MBytes).
- Maradidou S. (2010) "Molecular dynamics simulations of the peptide AAGDYY", Diploma thesis (PDF 1.1 MBytes).
- Kokkinidou M. (2010) "Homology modelling and molecular dynamics simulations of a homotetrameric Rop variant", Diploma thesis (PDF 4.1 MBytes).
- Koutsovoulos G. (2008) "HMDock: A computer program for homology modelling and docking", Diploma thesis (PDF 1.5 MBytes).
- Pougounia A. (2007) "Computational studies of the native Rop protein", Diploma thesis (PDF 3 MBytes).
- Palitskaris D. (2007) "Peptide-nucleic acids interactions: molecular dynamics simulations of the EcoRI's recognition peptide and its cognate sequence", Diploma thesis.
- Papaioannou H. (2007) "Molecular dynamics studies of a Rop variant with a re-designed hydrophobic core: Ala(2) Ile(2) -6", Diploma thesis (PDF 8.0 MBytes).
- Georgoulia P. (2006) "Molecular dynamics simulations of an artificial 4-α-helical bundle: Ala(2) Leu(2) -8", Diploma thesis (PDF 5.5 MBytes).
Recent conference posters
- Melas A. & Glykos, N.M. (2026) "Automating the multidimensional clustering of data derived from a Principal Component Analysis of molecular dynamics trajectories using HDBSCAN", EEBMB conference (Poster).
- Zigkou, A.-M. & Glykos, N.M. (2024) "Folding of the human Pin1 WW domain using molecular dynamics simulations", EEBMB conference (Abstract, Poster).
- Touliopoulos, S. & Glykos, N.M. (2023) "Atomic density distributions in proteins: structural and functional implications", 11th HeCrA conference, HSCBB23 conference (Abstract, Poster), EEBE conference (Poster).
- Chatzopoulou, M. & Glykos, N.M. (2021) "Geometric modeling of coiled-coils using Isambard: the case of the RM6 variant of the Repressor of Primer protein", HSCBB21 conference (Abstract, Poster).
- Giannaki, A.-A. & Glykos, N.M. (2021) "Buried β-turns in hydrophobic cores: Structural and Functional Implications", HeCrA conference (Abstract, Poster).
- Mitsikas, D. & Glykos, N.M. (2018) "Propensities of Asn-Gly heptapeptides to form β-turn structures: a Molecular Dynamics simulation approach", HeCrA-HSCBB conference (PDF 1.9 MBytes).
- Moschou, D. & Glykos, N.M. (2016) "Approaching the crystallographic phase problem with Artificial Neural Networks", HeCrA-HSCBB conference (PDF 0.5 MBytes).
- Riziotis, I. & Glykos, N.M. (2016) "Two-residue periodicities in protein structures : Results from a systematic search in 4-dimensional Ramachandran space", HeCrA-HSCBB conference, HSBMB conference (PDF 2.0 MBytes).
- Baltzis, A. & Glykos, N.M. (2014) "Multidimensional PCA-based clustering of molecular dynamics trajectories", HeCrA conference (PDF 0.2 MBytes).
- Serafeim A.-P. & Glykos, N.M. (2014) "Molecular Dynamics Simulations of a Ten-Amino Acid Protein", HeCrA conference (PDF 0.8 MBytes).
- Patmanidis, I. & Glykos, N.M. (2012) "Folding simulations of a highly frustrated peptide", HSCBB conference (PDF 1.2 MBytes).