Optimization and design
Overview
The two most widely-used software packages for protein design are Rosetta and (to a much lesser extent) Osprey.
Rosetta
Background
Weights
talaris2013
talaris2014
beta_nov15
Protocols
relax
score
fixbb basic
fixbb.static.linuxgccrelease \
-in:file:s '{structure_file}' \
-database '{rosetta_db}' \
-dun10 \
-scorefile 'default_{structure_file}' \
-out:suffix '_def' \
-beta_nov16_cart
fixbb extended
fixbb.static.linuxgccrelease \
-in:file:s '{structure_file}' \
-database '{rosetta_db}' \
-resfile '{res_file}' \
-dun10 \
-ex1 \
-ex2 \
-extrachi_cutoff 0 \
-minimize_sidechains True \
-scorefile 'fixbb_{structure_file}' \
-beta_nov16_cart \
-relax:fast
ddg_monomer
https://www.rosettacommons.org/docs/latest/application_documentation/analysis/ddg-monomer
ddg_monomer.static.linuxgccrelease \
-in:file:s '{structure_file}' \
-in::file::fullatom \
-database '{rosetta_db}' \
-ignore_unrecognized_res true \
-ignore_zero_occupancy false \
-fa_max_dis 9.0 \
-ddg::weight_file soft_rep_design \
-ddg::mut_file '{mutation_file}' \
-ddg::iterations 50 \
-ddg::local_opt_only true \
-ddg::dump_pdbs true \
-ddg::suppress_checkpointing true \
-ddg::mean true \
-ddg::min true \
-ddg::output_silent true