Figure 7.

Structural model of hDus2, a representative of DUS family. In this model, domains do not interact with each other and are positioned arbitrary (the N-terminal domain on the right, the C-terminal domain on the left), to facilitate visual analysis of binding site. Coordinates are available for download from the FTP server ftp://genesilico.pl/iamb/models/hdus2/ webcite (A) Protein shown in a ribbon representation colored according to the estimated accuracy of individual residues calculated by MetaMQAP (Blue indicates low predicted deviation of Cα atoms down to 0 Å, red indicates unreliable regions with deviation > 5 Å; see Methods for details). (B) Model backbone shown in the ribbon representation, conserved residues in the active site are labeled and shown in the space-filled representation. For clarity of the presentation, each residue is shown in a different color. (C) Protein in a surface representation colored according to sequence conservation in the DUS family, calculated from a multiple sequence alignment using CONSURF [27]. Blue indicates conserved residues, yellow to red indicated variable residues. (D) Protein in a surface representation, colored according to the distribution of the electrostatic potential, calculated with the APBS software (Adaptive Poisson-Boltzmann Solver) [28] available via PyMOL [29]. Blue indicates positively charged regions (11 kT), red indicated negatively charged regions (−11 kT). The same view as in the model and its features were visualized with PyMOL [29].

Kasprzak et al. BMC Bioinformatics 2012 13:153   doi:10.1186/1471-2105-13-153
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