Active members
Other than NMG, the group presently comprises Roubeas Ilias (xtcv : a lightweight molecular graphics viewer for XTC trajectories, BSc), Tsevis Aggelos (NOEmd : a computer program to automate the comparison between experimental NMR data and molecular dynamics simulations, BSc), Tsabazi Vasiliki (A memory-efficient method for quantifying convergence of molecular dynamics trajectories, BSc), Sviggou Nikoleta (The Repressor of Primer protein : to be native-like, or not to be ? Comparative computational studies of the D30P vs A31P mutants, BSc), Karapostoli Georgia (How protein turns unfold : molecular dynamics simulations of a ROP protein variant carrying a partially unfolded turn, BSc), Prigkou Ioanna (Quantifying the effect of mutations on protein stability using molecular dynamics simulations : the case of the D30G ROP mutant, BSc), Zachariadis Anastasios (In silico folding of a three-stranded β-sheet peptide with aromatic cross-links, 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, Password protected, available upon request).
- 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
- 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
- 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
- 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).