The HIVToolbox 2 Web System Integrates Sequence, Structure, Function and Mutation Analysis
Synchronized structure windows of HIV protease:Saquinavir complex (1C6Z; chain A; A–F) and information tables (G–H). The coloring schemes are: A. Domains and motifs are colored in the Domain/Motif window as defined in the Log windows (not shown). B. Functional sites and protein-protein interactions are colored in the Protein Interactions/Sites window C. Conservation of the residues is shown in the Homology window. The conservation slide threshold is set to 99% amino acid identity and yellow residues are conserved among 50,017 viral sequences shown here. D. DRM window with DRMs for Saquinavir colored. The coloring scheme for the DRMs is beneficial (green), beneficial set (light green), primary (red), primary set (pink), secondary set (purple) G. Information for each DRM is shown in a table that is color coded using the same DRM coloring scheme. DRMs for different drugs can be loaded using the pulldown menu at the bottom of the table. This table also provides the original amino acid, position, mutated amino acid, and links to the abstracts of PubMed papers supporting the DRM. The first column of this table is interactive, where a mouse click identifies the amino acid in the structure of the DRM window (D). E. Drug Binding Site window showing the structure of protease with the binding site for Saquinavir colored. The coloring scheme for the DRMs is as in Fig. 2 with an additional orange color for binding site residues that do not have a known DRM (orange). H. Information for each Drug Binding Site Residue is shown in a table that is color-coded using the same coloring scheme as in E. A distance threshold between atoms of the drug and atoms of the protein (2.5–4.0 Å) can be set using a pulldown menu; 4.0 Å was set in this figure. This table provides the amino acid position, shortest distance to a drug atom, whether it is a DRM, and the type of DRM. The first column of this table is interactive, where a mouse click identifies the amino acid in the structure of the Drug Binding Site window (E). F. Epitope window showing protease with the immune epitope KMIGGIGGFI colored green. Different positive immune epitopes for the loaded HIV protein from the IEDB can be selected using a pulldown menu on the top of the window that shows the IEDB id number and peptide sequence4.