The scripts and input files that accompany this demo can be found in the
demos/public directory of the Rosetta weekly releases.
KEYWORDS: PEPTIDES DESIGN
written by Kevin Drew (Bonneau Lab), firstname.lastname@example.org
This demo shows how to run the oop_design application. An oligooxopiperazine (oop) is a helical mimetic scaffold used for inhibiting protein interactions. The demo shows the design of an oop inhibitor for the MDM2-P53 protein interaction.
for example, you can run (where
$> $ROSETTA3/bin/oop_design.default.linuxgccrelease @inputs/flags
./input/flags = user specified options ./input/mdm2_oopAAAA.pdb = input structure where target is chain 1 and oop is chain 2
-oop_design_positions = residues on oop to design (numbering is relative to oop, for example 3 is the third residue on oop), default repacks with no design -pert_num = number of pertubations during pertubation phase, default 10, production 100 -design_loop_num = number of pertubation + design cycles, default 10, production 10 -nstruct = production 1000
Similar to other multi chain design protocols, the ddG is computed and is a good indicator of a good design. First sort by total score, take top 5 percent and then sort by REPACK_ENERGY_DIFF.
This app is inflexible to adjusting monte carlo temperatures, score functions, degree of rigid body pertubations, designing noncanonical amino acids, etc. The app also requires the oop is close to a plausible binding mode with respect to the target.