Prime User Manual - ISP

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Chapter 7: Prime–Refinement
7. The 4 best new structures are taken as input for resampling, starting from Step 2. The process
is repeated until convergence is obtained.
7.9.3 Side-Chain Prediction
The structure refinement program uses the following procedure to re-predict conformations for
the side chain set that you select.
1. Side-chain rotamers are randomized for nonconserved residues (the default) or for all residues.
2. Beginning with the first residue to be predicted, the side-chain rotamer library is used to
find the rotamer with the lowest energy while keeping all other side chains fixed. Once
the process is complete for the first residue, the next residue is treated, and so forth until
all have been done once (a single pass has been completed).
3. Once the pass is complete, Step 2 is repeated from the beginning, and then repeated again
until the side-chain rotamers appear to be converged (no more changes are occurring).
4. Minimization is run on all of the side-chain atoms (but not backbone atoms) of the residues
being treated.
7.10 Refinement with Nonstandard Residues
If you want to refine a structure with nonstandard residues, you can make changes to the residues
in the structures before refinement. Several nonstandard residues are supported in the
Build panel: the neutralized forms of ASP, LYS, ARG, and GLU, which are named ASH, LYN,
ARN, and GLH; and the tautomers of HIS (HID=HIS and HIE) and its protonated form, HIP.
Ionization (deprotonation) of four other residues are supported, CYS, SER, THR, and TYR.
The names of the ionized residues are CYT (thiolate), SRO (alkoxide), THO (alkoxide), and
TYO (phenoxide). In addition, the disulfide-bridged CYS is supported as CYX. To change one
of these residues, you can either change the name, or change the structure. For example, you
can generate an ionized SER by either of the following methods:
• Changing the residue name to SRO. The HG is deleted and a formal negative charge is
added to the OG.
• Deleting the HG (if present) and adding a formal charge to the OG. The residue is
renamed to SRO.
Prime 2.1 User Manual