PLoS ONE. 2008; 3(1): e1485
Protein Modelling The software packages YASARA (www.yasara.org) and Deep View Swiss-PDB Viewer (www.expasy.org/spdbv) were used to model changes in the P2 domain 3D structure. The previously published crystal structure of norovirus strain VA387 was used in the analysis and is available as a PDB file from www.rcsb.org, DOI 10.2210/pdb2obs/pdb [24].
PLoS ONE. 2008; 3(1): e1485
Figure 3 Conformational P domain (strain VA387) showing positions of potentially significant variation hotspots. Hotspots identified as significant amino acid changes were mapped onto the crystal structure of strain VA387. Sites A and B are coloured magenta. RGD motif associated with the binding pocket described by Tan et al [25] is coloured yellow. The RGD motif associated with the epidemic in 2002 described in this paper is coloured gray. The sugar molecule indicates the position of the putative binding site proposed by Cao et al [24]. PLoS ONE. 2008; 3(1): e1485.
BMC Genomics. 2008; 9: 44
Structure model The model of complex of plant CCCH protein with the RNA nonamer was constructed using the Swiss-Model programs [70]. The final merged files was presented and annotated with Swiss Pdb Viewer 3.7 and Rastop 2.2.
J Physiol. 2006 March 1; 571(Pt 2): 287–302.
Figure 5 Location of Kir2.1 mutations used in the study A and B, crystal structure of C terminus of Kir2.1 channel (Pegan et al. 2005) was visualized using Swiss-PDB Viewer software. Two opposing subunits were removed for clarity and side chains for the mutants used in this study displayed. A represents a side view, and B shows a top view of the pore region. C, sequence alignment of Kir2 channels in the region around the residues critical for inward rectification. Arrowhead points to the highly conserved F254 residue and asterisk indicates the least conserved site in this region. J Physiol. 2006 March 1; 571(Pt 2): 287–302.
