Download Task #2—Script File

SMART Team Qualification Model Design Detail Sheet
SMART Team:
SMART Team Mentor Name(s):
Protein Name:
Task #2—Script File
PDB File:
Due: Friday, January 16th
JpgDesigning
filename: your model
For Task #2, please submit a preliminary model design and model detail sheet describing the features of
Which
youshould
include
on on conversations that you had with your mentor about the
your features
model. Thisdid
design
be based
function
of
the
protein,
information
that
you have read in the articles related to your protein of interest,
your model and which specific colors
as well as any specific design features that he or she may have in mind.
were used to highlight these features?
(please be sure to indicate ALL colors
in your model, including colors
selected for hydrogen bonds and
struts)
Which amino acids are displayed and
WHY
didquestions
you display
(what
role
A few
to helpthem
guide you
as you
design your model. Please note – not all of these suggestions
are
applicable
to
all
biomolecules/PDB
files.
do these amino acids play in the
1. What story would you like to tell with your model? If the protein is an enzyme, is there an active
function
of the protein)?
site? Is it a binding protein? Does it interact with another protein? Or with DNA?
2. Which sidechains do you want to display? And what is the reason for displaying these
sidechains? (What is their function?)
3. Is there a heterologous group that should be included within the model? An inhibitor or a
substrate or other items?
4. What other features do you want to highlight – the secondary structures? A binding domain?
5. Which colors do you want to use? Remember to include the colors in your model description
information.