Hanne Verswyvel

Chapter 4 │ Page 152 39. Abraham, M.J., et al., GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX, 2015. 1: p. 19-25. 40. Schmid, N., et al., Definition and testing of the GROMOS force-field versions 54A7 and 54B7. European biophysics journal, 2011. 40(7): p. 843-856. 41. Petrie, E.J., et al., CD94-NKG2A recognition of human leukocyte antigen (HLA)-E bound to an HLA class I leader sequence. The Journal of experimental medicine, 2008. 205(3): p. 725-735. 42. Fan, Q.R., et al., Crystal structure of the human natural killer cell inhibitory receptor KIR2DL1–HLA-Cw4 complex. Nature immunology, 2001. 2(5): p. 452-460. 43. Petrov, D., et al., A systematic framework for molecular dynamics simulations of protein post-translational modifications. PLoS computational biology, 2013. 9(7): p. e1003154. 44. Berendsen, H.-J., et al., The missing term in e ective pair potentials. Journal of Physical Chemistry, 1987. 91(24): p. 6269-6271. 45. Bussi, G., et al., Canonical sampling through velocity rescaling. The Journal of chemical physics, 2007. 126(1). 46. Parrinello, M., et al., Polymorphic transitions in single crystals: A new molecular dynamics method. Journal of Applied physics, 1981. 52(12): p. 7182-7190. 47. Tironi, I.G., et al., A generalized reaction field method for molecular dynamics simulations. The Journal of chemical physics, 1995. 102(13): p. 5451-5459. 48. Humphrey, W., A. Dalke, and K. Schulten, VMD: visual molecular dynamics. Journal of molecular graphics, 1996. 14(1): p. 33-38. 49. Kästner, J., Umbrella sampling. Wiley Interdisciplinary Reviews: Computational Molecular Science, 2011. 1(6): p. 932-942. 50. Hub, J.S., et al., A Free Weighted Histogram Analysis Implementation Including Robust Error and Autocorrelation Estimates. Journal of chemical theory and computation, 2010. 6(12): p. 3713-3720. 51. Margreitter, C., et al., Vienna-PTM web server: a toolkit for MD simulations of protein post-translational modifications. Nucleic acids research, 2013. 41(W1): p. W422W426. 52. Takai, E., et al., Chemical modification of amino acids by atmospheric-pressure cold plasma in aqueous solution. Journal of Physics D: Applied Physics, 2014. 47(28): p. 285403. 53. Zhou, R., et al., Interaction of atmospheric-pressure air microplasmas with amino acids as fundamental processes in aqueous solution. PloS one, 2016. 11(5): p. e0155584. 54. Wenske, S., et al., Nonenzymatic post-translational modifications in peptides by cold plasma-derived reactive oxygen and nitrogen species. Biointerphases, 2020. 15(6). 55. Lins, L., A. Thomas, and R. Brasseur, Analysis of accessible surface of residues in proteins. Protein science, 2003. 12(7): p. 1406-1417. 56. Lin, A., et al., Acquired non-thermal plasma resistance mediates a shift towards aerobic glycolysis and ferroptotic cell death in melanoma. Drug Resistance Updates, 2023. 67: p. 100914. 57. Verswyvel, H., et al., Phototoxicity and cell passage a ect intracellular reactive oxygen species levels and sensitivity towards non-thermal plasma treatment in fluorescentlylabeled cancer cells. Journal of Physics D: Applied Physics, 2023. 56(29): p. 294001.

RkJQdWJsaXNoZXIy MTk4NDMw