Prime User Manual - ISP

Chapter 7: Prime–Refinement
ment, with a 4 Å restriction on Cα movement. This is intended to sample the basins more
finely.
3. The eight refined structures from Step 2 are combined with the original structures from
Step 1, and this set of 16 structures is ranked by energy. The five top-scoring structures
are then subjected to a final stage of refinement, with a 2 Å restriction on Cα movement.
This is intended to perform fine-grained sampling of the best basins.
This procedure defines the “Extended High” sampling procedure. The “Extended Medium”
and “Extended Low” carry four and two structures, respectively, into Step 2 and Step 3.
In ultra-extended sampling, the three steps of extended sampling are followed by the steps
below.
4. The top four structures are selected, and two predictions run on each, with part of the loop
frozen. Runs are done with “moving windows” with varying numbers of contiguous residues:
all n residues, the two possible contiguous sets of n-1 residues, the three sets of n-2
residues, and so on. The structures are sorted after each cycle of a given number of residues.
5. Step 2 is repeated with the top eight structures cumulatively generated, then Step 3 is
repeated with the top eight structures cumulatively generated.
7.9.2 Cooperative Loop Refinement
Cooperative loop refinement proceeds as follows:
1. A list of side chains that will be optimized is generated. By default this list includes any
residue with an atom within 7.5 Å of either loop 1 or loop 2.
2. Loop 1 is sampled, allowing side chains in the list from Step 1 to move, holding the backbone
of loop 2 fixed at its original conformation. Eight loop conformations are generated.
3. Loop 2 is sampled, allowing side chains in the list from Step 1 to move, holding the backbone
of loop 1 fixed at its original conformation. Eight loop conformations are generated.
This step runs concurrently with Step 2.
4. Conformations of loop 1 from Step 2 with loop 2 from Step 3 are merged into a set of
structures.
5. All side chains in the list determined in Step 1 are reoptimized, keeping only those structures
whose energy is below the energy cutoff.
6. All residues in both loops are then minimized, including the backbone, keeping only
those structures whose energy is below the energy cutoff.
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