tr

TrDesign in JAX!

Work in Progress... For original version implemented in keras see: https://github.com/gjoni/trDesign/tree/master/02-GD

Google Colab

install

pip install git+https://github.com/sokrypton/ColabDesign.git@v1.1.1

# download weights
if [ ! -d params/tr ]; then
  mkdir -p params/tr
  wget -qnc https://files.ipd.uw.edu/krypton/TrRosetta/models.zip
  wget -qnc https://files.ipd.uw.edu/krypton/TrRosetta/bkgr_models.zip
  unzip -qqo models.zip -d params/tr/
  unzip -qqo bkgr_models.zip -d params/tr/
fi

example

from colabdesign import *

clear_mem()
tr_model = mk_trdesign_model(protocol="fixbb")
tr_model.prep_inputs(get_pdb("6MRR"), chain="A")
tr_model.design(100, verbose=10)
tr_model.plot()
print(tr_model.get_loss())
print(tr_model.get_seq())

example

combine AfDesign and TrDesign for fixed backbone design

from colabdesign import *

clear_mem()
af_model = mk_afdesign_model(protocol="fixbb")
af_model.prep_inputs(get_pdb("1TEN"))

tr_model = mk_trdesign_model(protocol="fixbb")
tr_model.prep_inputs(get_pdb("1TEN"))

af_model.restart()
af_model.design_3stage(callback=tr_model.af_callback())