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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

Osprey