Desmond Tutorial
Desmond Tutorial - DE Shaw Research
Desmond Tutorial - DE Shaw Research
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<strong>Desmond</strong> <strong>Tutorial</strong><br />
Preparing Proteins with Missing Residues or Side Chains<br />
Figure 3.6 Prime Find Homologs window<br />
Click the ‘Import’ button to read in<br />
the truncated 1su4 protein<br />
structure file so it can be used as<br />
a self-template.<br />
Now it is time to ʹfoolʹ Prime. Instead of reading the structures of sequence<br />
homologues to be used as structural templates—as we would do for comparative<br />
modeling—we will read in the truncated 1su4 protein structure file so it can<br />
be used as a self‐template.<br />
e. Click Import under Find Homologs.<br />
The Import Homolog From PDB File window appears as shown in Figure 3.7.<br />
Figure 3.7 Import Homolog From PDB File window in Prime<br />
Locate and select the<br />
truncated 1su4 protein<br />
structure file that has the<br />
missing residues.<br />
Click the ‘Import’<br />
button.<br />
f. Select the truncated 1su4 protein structure file that has the missing residues<br />
from the Files area. In this example, it is the 1su4_missing_loop.pdb file which<br />
was manually altered to remove residues 132–136. Click Import.<br />
34 D. E. Shaw Research September 2008