Page 127 - Read Online
P. 127
Page 16 of 16 Varming et al. Microbiome Res Rep 2024;3:15 https://dx.doi.org/10.20517/mrr.2023.50
aureus to livestock CC398. Front Microbiol 2017;8:2418. DOI PubMed PMC
30. Winn MD, Ballard CC, Cowtan KD, et al. Overview of the CCP4 suite and current developments. Acta Crystallogr D Biol Crystallogr
2011;67:235-42. DOI PubMed PMC
31. Vagin A, Teplyakov A. MOLREP : an automated program for molecular replacement. J Appl Crystallogr 1997;30:1022-5. DOI
32. Vagin AA, Steiner RA, Lebedev AA, et al. REFMAC5 dictionary: organization of prior chemical knowledge and guidelines for its use.
Acta Crystallogr D Biol Crystallogr 2004;60:2184-95. DOI PubMed
33. Emsley P, Lohkamp B, Scott WG, Cowtan K. Features and development of Coot. Acta Crystallogr D Biol Crystallogr 2010;66:486-
501. DOI PubMed PMC
34. Lovell SC, Davis IW, Arendall WB III, et al. Structure validation by Cα geometry: ϕ, ψ and Cβ deviation. Proteins 2003;50:437-50.
DOI PubMed
35. Varadi M, Anyango S, Deshpande M, et al. AlphaFold Protein Structure Database: massively expanding the structural coverage of
protein-sequence space with high-accuracy models. Nucleic Acids Res 2022;50:D439-44. DOI PubMed PMC
36. Mirdita M, Schütze K, Moriwaki Y, Heo L, Ovchinnikov S, Steinegger M. ColabFold: making protein folding accessible to all. Nat
Methods 2022;19:679-82. DOI PubMed PMC
37. Rohmer C, Dobritz R, Tuncbilek-Dere D, et al. Influence of Staphylococcus aureus strain background on Sa3int phage life cycle
switches. Viruses 2022;14:2471. DOI PubMed PMC
38. Rezaei Javan R, Ramos-Sevillano E, Akter A, Brown J, Brueggemann AB. Prophages and satellite prophages are widespread in Streptococcus
and may play a role in pneumococcal pathogenesis. Nat Commun 2019;10:4852. DOI PubMed PMC
39. Matos RC, Lapaque N, Rigottier-Gois L, et al. Enterococcus faecalis prophage dynamics and contributions to pathogenic traits. PLoS
Genet 2013;9:e1003539. DOI PubMed PMC

