Biomedical Engineering Reference
In-Depth Information
Fig. 12.2
(
a
) Overlay of FlexX-docked pose of
h4
and X-ray pose of biotin in the aptamer RNA
pseudoknot. The ligand is rendered in capped stick. Carbon atoms of
h4
are
magenta
and those of
biotin are
white
.
Cyan
lined-ribbon represents the backbone of RNA. (
b
) Docked model of
h4
in
complex with biotin-pseudoknot complex. The residues in the active site are rendered in stick.
Carbon atoms of pseudoknot are
green
,
oxygen red
,
nitrogen blue
, and
phosphorus orange
.
Yellow
dashed lines
are hydrogen bonds
Fig. 12.3
(
a
) Two-dimensional model of SARS-pseudoknot generated by the PSEUDOVIEWER
program. (
b
) Three-dimensional structural model of the SARS-pseudoknot used in this study. It
was optimized by molecular dynamics simulation using the Amber 8.0 program.
Brown ribbon
renders the phosphate backbone of the RNA pseudoknot
Based on these successful results, Park applied the virtual screening strategy to
discover ligands for the SARS-pseudoknot, even though its 3D structure was not
completely determined. It was known that the SARS-pseudoknot has a unique 3
stem-3 loop structure. They built a 3D model using the RNA pseudoknot predicting
program (PSEUDOVIEWER) and Sybyl molecular modeling software, and then
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