Desmond Tutorial

Desmond Tutorial
Preparing Proteins with Missing Residues or Side Chains
To run Prime:
1. Download the 1su4 structure as shown in Figure 1.4 on page 5. This structure has all
residues present in the PDB file, but as a working example, we will delete a small
loop by hand‐editing the PDB file.
2. Delete residues 132–136 from the 1su4 PDB file by hand (the original PDB file should
be in the working directory after the download) and save it as
1su4_missing_loop.pdb.
3. Import the modied PDB structure into Maestro as shown on Figure 1.3 on page 4.
The truncated structure replaces the full structure in the Workspace where the missing
loop is called out in a red box in Figure 3.1.
Figure 3.1 Missing loop in the 1su4 protein
The loop between the two
orange ribbons is
missing.
The white gaps in the
residues (shown in green)
represents the missing
loop.
NOTE
NOTE
4. Apply Prime to the truncated 1su4 protein structure with the missing loop.
Running Prime can be computationally intensive. To save time, you can distribute Prime
jobs among multiple CPUs.
If your protein only has missing side chains (no missing residues), you can select the Predict
side chains task under Applications > Prime > Refinement to automatically fill in the
missing residues without running the entire Prime structure prediction protocol as
shown in Figure 3.2.
30 D. E. Shaw Research September 2008