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This was made with Doug Daniels for a journal cover. It illustrates his findings
of how a particular DNA binding protein attaches to DNA molecule, binding on the
minor groove side rather than the usual minor groove side, and flipping out one of
the DNA bases in the process. This is a figure uses fully custom geometries created
with CAD-Zilla, and strung into the DNA shape using a Jython script, over a
Vincent van Mol protein data structure.
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These figures were made for Rosa Cardoso. They show the progress of trans-membrane protein. They were made using Vincent van Mol and CAD-Zilla.
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A very long coiled wound peptide helix, done with Vincent van Mol.
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This is a figure made for Li Fan, showing a DNA binding protein bound to a section
of a the DNA molecule. The DNA molecule is rendered as Vincent van Mol ribbon in
red and purple. The DNA is rendered with Vincent van Mol, using the tube and ball
and stick geometries.
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These figures were made with Victoria Roberts. Like many of the
figures made for the labs these figures show a DNA binding protein
in action. This figure is particularly interesting because of the
way the DNA geometry was made. Rather than just stringing a
ribbon through the coordinates in a PDB file, the DNA geometry
was made with some custom geometrical operations. An extrusion
was made using CAD-Zilla. The extrusion was twisted using a space
for application module (which we have not released on the Web
site). The twisted expression was then bent using the space warp
module. The twisting and unbending was done in such a way so as
to exactly match the DNA coordinates in a PDB file. The result
was a nifty way to look at a DNA molecule. This geometry works
particularly well as a physical model constructed in a stereo lithography printer.
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These figures were made with Victoria Roberts. They show a DNA
molecule surfaced around the PDB coordinate file with colors
corresponding to any electrostatic potential field. The DNA
molecule was then "untwisted" using the space warp module. This
enables one to see the electrostatic potential patterns of the
major or minor groove in one picture, rather than having to spend
it would the DNA around interactively. One can then discern
patterns that they may have not noticed looking at the DNA in
it's natural twisted form.
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This is an ancient shark tooth from a fossil. A German scientist
made the picture using GridZilla.
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