Tutorial 4.5 Additional features

Introduction

In this tutorial you will learn how to use LIT-AF to modify the monomer objects by:

• Removing a user defined region of the MSA
• Cutting the monomer (as in the original AlphaPulldown)
• Removing all monomer MSA features
• Removing template features

To run this tutorial the outputs from Tutorial 1 (CXCR4.pkl) will be used.

MSA removal from a specfic region

This method removes part of the MSA of a monomer to force AlphaFold to relay more on template information, or to eliminate interaction between different domains of the same monomer. The calculations can be run in two different ways:

• By specifing in the input file where to remove the MSA for each monomer

- {protein_name: CXCR4_active_state,  remove_msa_region: 1-300}

python $LITAF/run_multimer_jobs.py \
output_path=test_structure \
monomer_objects_dir=[../tutorial_1_2/protein_features_mmseqs2] \
input_file=[monomer_multistate.in.yaml] \
run.only_template=True

• By applying the change to ALL the objects present in the input file as in monomer_annotated.in.yaml

CXCR4_active_state
CXCR4_inactive_state

python $LITAF/run_multimer_jobs.py \
output_path=test_structure \
monomer_objects_dir=[../tutorial_1_2/protein_features_mmseqs2] \
input_file=[monomer_annotated.in.yaml] \
only_template=True \
remove_msa_region='1-300'

This method is more indicated for large scale calculations to not have to write large input files with the same options.

Generating chopped monomer

This method allows to remove part of the input sequence from an already generated monomer object in case it is necessary to model only a smaller part of the origianl protein, or ot remove unfolded regions causing issues during structure prediction. To cut a monomer it is sufficient to add the keyword selected_residues in the input file followed by the number of the residues to keep in the chopped monomer.

- {protein_name: CXCR4,  selected_residues: 1-300}

Removing all monomer MSA features

This method removes all monomer MSA features obtaining results based only on template information. The calculations can be run in two different ways:

• By specifing the specific targets in the input file using the remove_monomer_msa keyword

- {protein_name: CXCR4, remove_monomer_msa: True}

• By applying the change to ALL the objects present in the input file as in the file monomer_annotated.in

CXCR4_active_state
CXCR4_inactive_state

python $LITAF/run_multimer_jobs.py \
output_path=test_structure \
monomer_objects_dir=[../tutorial_1_2/protein_features_mmseqs2] \
input_file=[monomer_annotated.in.yaml] \
only_template=True \
remove_unpaired_msa=True

This method is more indicated for large scale calculations to not have to write large input files with the same options.

Removing template features

This method removes all template features obtaining results based only on MSA information. The calculations can be run in two different ways:

• By specifing the targets using the keyword remove_templates

- {protein_name: CXCR4 remove_templates: True}

• By applying the change to ALL the objects present in the input file as in the file monomer_annotated.in

CXCR4_active_state
CXCR4_inactive_state

python $LITAF/run_multimer_jobs.py \
output_path=test_structure \
monomer_objects_dir=[../tutorial_1_2/protein_features_mmseqs2] \
input_file=[monomer_annotated.in.yaml] \
run.use_templates=False

This method is more indicated for large scale calculations to not have to write large input files with the same options.

Conclusion

In this tutorial you have learned how to remove specific region of monomer MSA and how to generated a chopped verion of the original monomer.