Nicholas M. Glykos' group

54. Vouzina, O.-D., Tafanidis, A. & Glykos*, N.M. (2024), "The curious case of A31P, a topology-switching mutant of the Repressor of Primer protein : A molecular dynamics study of its folding and misfolding", arXiv:2404.01405 [q-bio.BM]. (abstract, PDF 2.3 MBytes).

53. Kolocouris*, A., Arkin, I. & Glykos*, N.M. (2022), "A proof-of-concept study of the secondary structure of influenza A, B M2 and MERS- and SARS-CoV E transmembrane peptides using folding molecular dynamics simulations in a membrane mimetic solvent", Phys. Chem. Chem. Phys., 24, 25391-25402. (abstract, PDF 1.8 MBytes).

52. Gkogka, I. & Glykos*, N.M. (2022), "Folding molecular dynamics simulation of T-peptide, a HIV viral entry inhibitor : Structure, dynamics, and comparison with the experimental data", J. Comput. Chem., 43, 942-952. (abstract, PDF 18 MBytes).

51. Mitsikas, D.A. & Glykos*, N.M. (2020), "A molecular dynamics simulation study on the propensity of Asn-Gly-containing heptapeptides towards β-turn structures: Comparison with ab initio quantum mechanical calculations", PLoS ONE, 15(12): e0243429. (abstract, PDF 2.8 MBytes).

50. Kokkinidis, M., Glykos*, N.M. & Fadouloglou*, V.E. (2020), "Catalytic activity regulation through post-translational modification: the expanding universe of protein diversity", Adv. Protein Chem. Struct. Biol., 122, 97-125. (abstract, PDF 2.5 MBytes).

49. Stylianakis, I., Shalev, A., Scheiner, S., Sigalas, M.P., Arkin, I.T., Glykos*, N.M. & Kolocouris*, A. (2020), "The balance between side‐chain and backbone‐driven association in folding of the α‐helical influenza A transmembrane peptide", J. Comput. Chem., 41, 2177-2188. (abstract, PDF 3.1 MBytes).

48. Riziotis, I.G. & Glykos*, N.M. (2019), "On the presence of short-range periodicities in protein structures that are not related to established secondary structure elements", Proteins, 87, 966-978. (abstract, PDF 5.7 MBytes).

47. Georgoulia, P.S. & Glykos*, N.M. (2019), "Molecular simulation of peptides coming of age: Accurate prediction of folding, dynamics and structures", Arch. Biochem. Biophys., 664, 76-88. (abstract, PDF 1.6 MBytes).

46. Georgoulia*, P.S. & Glykos, N.M. (2018), "Folding Molecular Dynamics Simulation of a gp41-Derived Peptide Reconcile Divergent Structure Determinations", ACS Omega, 3, 14746-14754. (abstract, PDF 1.7 MBytes).

45. Adamidou, T., Arvaniti, K.-O. & Glykos*, N.M. (2018), "Folding Simulations of a Nuclear Receptor Box-Containing Peptide Demonstrate the Structural Persistence of the LxxLL Motif Even in the Absence of Its Cognate Receptor", J. Phys. Chem. B, 122, 106−116. (abstract, PDF 2.5 MBytes).

44. Fadouloglou, V.E., Balomenou, S., Aivaliotis, M., Kotsifaki, D., Arnaouteli, S., Tomatsidou, A., Efstathiou, G., Kountourakis, N., Miliara, S., Griniezaki, M., Tsalafouta, A., Pergantis, S.A., Boneca, I.G., Glykos, N.M., Bouriotis, V. & Kokkinidis*, M. (2017), "An unusual α-carbon hydroxylation of proline promotes active-site maturation", J. Am. Chem. Soc., 139, 5330–5337. (abstract, PDF 2.5 MBytes).

43. Serafeim, A.-P., Salamanos, G., Patapati, K.K. & Glykos*, N.M. (2016), "Sensitivity of Folding Molecular Dynamics Simulations to Even Minor Force Field Changes", J. Chem. Inf. Model., 56, 2035-2041. (abstract, PDF 2.6 MBytes).

42. Baltzis, A.S. & Glykos*, N.M. (2016), "Characterizing a partially ordered miniprotein through folding molecular dynamics simulations: Comparison with the experimental data", Prot. Sci., 25, 587–596. (abstract, PDF 3.3 MBytes).

41. Baltzis, A.S., Koukos, P.I. & Glykos*, N.M. (2015), "Clustering of molecular dynamics trajectories via peak-picking in multidimensional PCA-derived distributions", arXiv:1512.04024 [q-bio.BM]. (abstract, PDF 826 KBytes).

40. Koukos, P.I. & Glykos*, N.M. (2014), "Folding Molecular Dynamics Simulations Accurately Predict the Effect of Mutations on the Stability and Structure of a Vammin-Derived Peptide", J. Phys. Chem. B, 118, 10076–10084. (abstract, PDF 3.7 MBytes).

39. Koukos, P.I. & Glykos*, N.M. (2014), "On the application of Good-Turing statistics to quantify convergence of biomolecular simulations", J. Chem. Inf. Model., 54, 209-217. (abstract, PDF 1.1 MBytes).

38. Koukos, P.I. & Glykos*, N.M. (2013), "grcarma: A Fully Automated Task-Oriented Interface for the Analysis of Molecular Dynamics Trajectories", J. Comput. Chem., 34, 2310-2312, Cover story for Vol.34, Issue 26. (abstract, PDF 929 KBytes).

37. Kontopoulos, D.-G. & Glykos*, N.M. (2013), "Pinda: A Web service for detection and analysis of intraspecies gene duplication events", Comput. Methods Programs Biomed., 111, 711-714. (abstract, PDF 729 KBytes).

36. Georgoulia, P.S. & Glykos*, N.M. (2013), "On the Foldability of Tryptophan-Containing Tetra- and Pentapeptides: An Exhaustive Molecular Dynamics Study", J. Phys. Chem. B, 117, 5522–5532. (abstract, PDF 3.1 MBytes).

35. Patmanidis, I. & Glykos*, N.M. (2013), "As good as it gets? Folding molecular dynamics simulations of the LytA choline-binding peptide result to an exceptionally accurate model of the peptide structure", J. Mol. Graph. Model., 41, 68-71. (abstract, PDF 686 KBytes).

34. Fadouloglou, V.E., Kapanidou, M., Agiomirgianaki, A., Arnaouteli, S., Bouriotis, V., Glykos*, N.M. & Kokkinidis*, M. (2013), "Structure determination through homology modelling and torsion-angle simulated annealing: application to a polysaccharide deacetylase from Bacillus cereus", Acta Crystallogr., D69, 276-283. (abstract, PDF 2.4 MBytes).

33. Kokkinidis, M., Glykos, N.M. & Fadouloglou*, V.E. (2012), "Protein Flexibility and Enzymatic Catalysis", Adv. Protein Chem. Struct. Biol., 87, 181-218. (abstract, PDF 562 KBytes).

32. Georgoulia, P.S. & Glykos*, N.M. (2011), "Using J-coupling constants for force field validation: Application to hepta-alanine", J. Phys. Chem. B, 115, 15221–15227. (abstract, PDF 3.6 MBytes).

31. Patapati, K.K. & Glykos*, N.M. (2011), "Three Force Fields' Views of the 310 Helix", Biophys. J., 101, 1766-1771. (abstract, PDF 805 KBytes).

30. Glykos*, N.M. (2011), "On the application of structure-specific bulk-solvent models", Acta Crystallogr., D67, 739-741. (abstract, PDF 982 KBytes).

29. Glykos*, N.M. (2011), "The 11th Misconception ? ", A letter to the Editor, CBE Life Sci Educ, 10(1), 1-2. (abstract, PDF 123 KBytes, Preprint with images (PDF 6.5 MBytes)).

28. Patapati, K.K. & Glykos*, N.M. (2010), "Order through Disorder: Hyper-Mobile C-Terminal Residues Stabilize the Folded State of a Helical Peptide. A Molecular Dynamics Study", PLoS ONE, 5, e15290. (abstract, PDF 607 KBytes).

27. Fadouloglou, V.E., Stavrakoudis, S., Bouriotis, V., Kokkinidis, M., & Glykos*, N.M. (2009), "Molecular Dynamics Simulations of BcZBP, A Deacetylase from Bacillus cereus: Active Site Loops Determine Substrate Accessibility and Specificity", J. Chem. Theory Comput., 5, 3299-3311. (abstract, PDF 7.3 MBytes).

26. Fadouloglou, V.E., Bastaki, M.N., Ashcroft, A.E., Phillips, S.E.V., Panopoulos, N.J., Glykos*, N.M., & Kokkinidis*, M. (2009), "On the quaternary association of the type III secretion system HrcQB-C protein: Experimental evidence differentiates among the various oligomerization models", J. Struct. Biol., 166, 214-225. (abstract, PDF 3.7 MBytes).

25. Fadouloglou, V.E., Kokkinidis, M. & Glykos*, N.M. (2008), "Determination of protein oligomerization state: Two approaches based on glutaraldehyde crosslinking", Anal. Biochem., 373, 404-406. (abstract, PDF 605 KBytes).

24. Mizas, Ch., Sirakoulis, G.Ch., Mardiris, V., Karafyllidis, I., Glykos, N.M. & Sandaltzopoulos*, R. (2008), "Reconstruction of DNA sequences using genetic algorithms and cellular automata: Towards mutation prediction ?", BioSystems, 92, 61-68. (abstract, PDF 574 KBytes).

23. Fadouloglou, V.E., Deli, A., Glykos, N.M., Psylinakis, E., Bouriotis, V. & Kokkinidis*, M. (2007), "Crystal structure of the BcZBP, a zinc-binding protein from Bacillus cereus. Functional insights from structural data", FEBS J., 274, 3044-3054. (abstract, PDF 1.2 MBytes).

22. Glykos*, N.M. (2007), "On the application of molecular-dynamics simulations to validate thermal parameters and to optimize TLS-group selection for macromolecular refinement", Acta Crystallogr., D63, 705-713. (abstract, PDF 1.4 MBytes).

21. Glykos*, N.M. (2006), "Carma: a molecular dynamics analysis program", J. Comput. Chem., 27, 1765-1768. (abstract, PDF 284 KBytes).

20. Glykos, N.M., Papanikolau, Y., Vlassi, M., Kotsifaki, D., Cesareni G. & Kokkinidis*, M. (2006), "Loopless Rop: Structure and Dynamics of an Engineered Homotetrameric Variant of the Repressor of Primer Protein", Biochemistry, 45, 10905-10919. (abstract, PDF 2.0 MBytes).

19. Glykos*, N.M. (2005), "Qs v.1.3: a parallel version of Queen of Spades", J. Appl. Crystallogr., 38, 574-575. (abstract, PDF 65 KBytes).

18. Glykos, N.M., & Kokkinidis*, M. (2004), "Structural Polymorphism of a Marginally Stable 4-alpha-Helical Bundle. Images of a Trapped Molten Globule ?", Proteins, 56, 420-425. (abstract, PDF 312 KBytes).

17. Papanikolau, Y., Kotsifaki, D., Fadouloglou, V.E., Gazi, A.D., Glykos, N.M., Cesareni G. & Kokkinidis*, M. (2004), "Ionic strength reducers: an efficient approach to protein purification and crystallization. Application to two Rop variants.", Acta Crystallogr., D60, 1334-1337. (abstract, PDF 539 KBytes).

16. Glykos*, N.M. & Kokkinidis, M. (2004), "Molecular Replacement with multiple different models", J. Appl. Crystallogr., 37, 159-161. (abstract, PDF 1.1 MBytes).

15. Fadouloglou, V.E., Tampakaki, A.P., Glykos, N.M., Bastaki, N., Hadden, J.M., Phillips, S.E., Panopoulos, N.J. & Kokkinidis*, M. (2004), "Structure of HrcQb-C, a conserved component of the bacterial type III secretion systems", Proc. Natl. Acad. Sci. USA, 101, 70-75. (abstract, PDF 629 KBytes).

14. Glykos*, N.M. & Kokkinidis, M. (2003), "Structure determination of a small protein through a 23-dimensional molecular replacement search", Acta Crystallogr., D59, 709-718. (abstract, PDF 3.8 MBytes).

13. Dennis, C.A., Glykos, N.M., Parsons, M.R. & Phillips*, S.E.V. (2002), "The structure of AhrC, the arginine repressor/activator protein from Bacillus subtilis", Acta Crystallogr., D58, 421-430. (abstract, PDF 1.6 MBytes).

12. Glykos*, N.M. & Kokkinidis, M. (2001), "Multidimensional Molecular Replacement", Acta Crystallogr., D57, 1462-1473. (abstract, PDF 1.9 MBytes).

11. Fadouloglou, V.E., Glykos, N.M., & Kokkinidis*, M. (2001), "Side-chain conformations in 4-alpha-helical bundles", Protein Engng., 14, 321-328. (abstract, PDF 385 KBytes).

10. Fadouloglou, V.E., Glykos*, N.M. & Kokkinidis, M. (2000), "A fast and inexpensive procedure for drying polyacrylamide gels.", Anal. Biochem., 287, 185-186. (abstract, PDF 69 KBytes).

9. Spyridaki, A., Glykos, N.M., Kotsifaki, D., Fadouloglou, V. & Kokkinidis*, M. (2000), "Crystallization and diffraction to ultrahigh resolution (0.8A) of a designed variant of the Rop protein.", Acta Crystallogr., D56, 1015-1016. (abstract, PDF 237 KBytes).

8. Glykos, N.M., & Kokkinidis*, M. (2000), "On the distribution of the bulk solvent correction parameters", Acta Crystallogr., D56, 1070-1072. (abstract, PDF 384 KBytes).

7. Glykos*, N.M. & Kokkinidis, M. (2000), "GraphEnt : a maximum entropy program with graphics capabilities.", J. Appl. Crystallogr., 33, 982-985. (abstract, PDF 777 KBytes).

6. Andreeva, A.E., Borissova, B.E., Mironova, R., Glykos, N.M., Kotsifaki, D., Ivanov, I., Krysteva, M. & Kokkinidis*, M. (2000), "Crystallization of type I chloramphenicol acetyltransferase : An approach based on the concept of ionic strength reducers", Acta Crystallogr., D56, 101-103. (abstract, PDF 319 KBytes).

5. Glykos*, N.M. & Kokkinidis, M. (2000), "A stochastic approach to Molecular Replacement", Acta Crystallogr., D56, 169-174. (abstract, PDF 415 KBytes).

4. Glykos*, N.M. (1999), "Pepinsky's Machine : an interactive, graphics-based Fourier synthesis program with applications in teaching and research.", J. Appl. Crystallogr., 32, 821-823. (abstract, PDF 660 KBytes).

3. Glykos, N.M. & Kokkinidis*, M. (1999), "Meaningful refinement of poly-alanine models using rigid-body simulated annealing: application to the structure determination of the A31P Rop mutant.", Acta Crystallogr., D55, 1301-1308. (abstract, PDF 1.7 MBytes).

2. Glykos, N.M., Cesareni, G. & Kokkinidis*, M. (1999), "Protein plasticity to the extreme : Changing the topology of a 4-alpha-helical bundle with a single amino-acid substitution.", Structure 7, 597-603. (abstract, PDF 2.2 MBytes).

1. Glykos, N.M., Holzenburg, A.K.H. & Phillips*, S.E.V. (1998), "Low resolution structural characterisation of the Arginine repressor/activator from Bacillus subtilis : A combined X-ray crystallographic and electron microscopical approach", Acta Crystallogr., D54, 215-225, and Acta Crystallogr., D54, 707-707. (abstract, PDF 2.6 MBytes).

0. Glykos, N.M. (1995), "Structural studies of the arginine repressor/activator from Bacillus subtilis", PhD thesis, Thesis advisor Prof Simon E.V. Phillips, Astbury Department of Biophysics, University of Leeds. (abstract, PDF 7.7 MBytes).