- V3 loop sequence space analysis suggests different evolutionary patterns of CCR5- and CXCR4-tropic HIVKatarzyna Bozek
Max Planck Institute for Informatics, Saarbrucken, Germany
PLoS ONE 4:e7387. 2009..Our study thus supports hypotheses of an association of immune system depletion with an increase in V3 loop sequence variability and with the escape of the viral sequence to distant parts of the sequence space...
- An expanded model of HIV cell entry phenotype based on multi-parameter single-cell dataKatarzyna Bozek
Department of Computational Biology and Applied Algorithmics, Max Planck for Computer Sciences, Campus E1 4 66123, Saarbrucken, Germany
Retrovirology 9:60. 2012....
- Analysis of physicochemical and structural properties determining HIV-1 coreceptor usageKatarzyna Bozek
Max Planck Institute for Computer Science, Saarbrucken, Germany
PLoS Comput Biol 9:e1002977. 2013..These regions are in close proximity in the bound conformation of the loop potentially forming a site determinant for the coreceptor binding. The method is available via server under http://structure.bioinf.mpi-inf.mpg.de/...
- A single amino acid substitution of the human immunodeficiency virus type 1 capsid protein affects viral sensitivity to TRIM5 alphaAyumu Kuroishi
Department of Viral Infections, Research Institute for Microbial Diseases, Osaka University, Osaka 565 0871, Japan
Retrovirology 7:58. 2010..This virus (NL-4/5S6/7SvifS) was supposed to escape from host restriction factors cyclophilin A, CM TRIM5 alpha, and APOBEC3G. However, the replicative capability of NL-4/5S6/7SvifS in human cells was severely impaired...
- Positive selection of HIV host factors and the evolution of lentivirus genesKatarzyna Bozek
Max Planck Institute for Informatics Computational Biology and Applied Algorithmics, Campus E1 4, 66123 SaarbrA 1 4 cken, Germany
BMC Evol Biol 10:186. 2010..Positive selection of host proteins that interact with pathogens can indicate factors relevant for infection and potentially be a measure of pathogen driven evolution...