Desmond Tutorial

Desmond Tutorial
Preparing Proteins with Missing Residues or Side Chains
Figure 3.12 Built in loop shown in the Workspace
The built-in loop
appears in the
Workspace.
m. Click Next in the Structure Prediction window.
At this point Refine Structure is highlighted in the workflow diagram at the bottom
of the window as shown in Figure 3.13.
Structure refinement includes loop refinement, side chain prediction, and simple
minimization. Side chain prediction is generally fairly reliable and loop prediction
is also reasonable up to 5–6 residues. Multiple loops can be refined
simultaneously.
n. Select the Refine loops task and in the Loops area of the window, select one or
more loops for refinement. Selected loops appear with yellow highlight as
shown in Figure 3.13. For this example, we select loop6 (131–137) which contains
the desired residues (132–136) as well as joining residues. You can handedit
the first and last residue of any loop in the table by double‐clicking the
value and entering a new one.
38 D. E. Shaw Research September 2008