Prime User Manual - ISP

66
Chapter 7: Prime–Refinement
• Unfreeze side chains within: Select this option to allow side chains near the specified loop
to move, and specify a distance in the text box. The default distance is 7.5 Å.
• Minimum allowed vdW overlap: By default, this value is set to 0.70, meaning that the distance
between atoms must be at least 70% of their ‘ideal’ van der Waals separation. The
extended sampling procedure tests multiple values for the minimum overlap, and therefore
this option is unavailable when extended sampling has been selected.
7.9 Technical Details for Refinement
7.9.1 Loop Refinement
Loop refinement using the Default option proceeds as follows:
1. The loop is reconstructed using the backbone dihedral library, by building up half from
each direction. The resolution starts off very coarsely, becoming finer until it manages to
produce a required number of physically realistic loop conformations (based on the
length of the loop).
2. The large number of loops generated in the first step are clustered, and representatives of
each cluster are selected.
3. These cluster representatives are then scored as follows:
a. Side chains are re-added to the loop residues, as well as any residues within a specified
cutoff, according to the side-chain optimization procedure.
b. The loop and contact side chains are minimized.
c. The energy is calculated.
4. The best scoring loop structures are returned.
Loop prediction with extended sampling is specifically designed to overcome sampling problems
with long loops, in which the number of residues results in an unwieldy number of
possible loop conformations.
Extended sampling uses the following procedure:
1. Two initial predictions are run on the loop. These are intended to coarsely sample conformational
space and are carried out with two slightly different sets of prediction parameters.
Each initial prediction returns up to four top-scoring conformations, resulting in up
to eight structures. These eight structures are intended as initial points for finer sampling
of what appears to be favorable regions (basins) of conformational space.
2. Each of the eight structures generated in Step 1 is run through another stage of refine-
Prime 2.1 User Manual