Tutorial 3 Monomer predictions

Introduction

LIT-AlphaFold was built on top of the architecture of AlphaPulldown which presents four different approaches to run calculations for large numbers of protein and protein multimers:

• Pulldown
• All vs all
• Custom
• Homo-oligomer

All calculations are performed using the run_multimer_jobs.py script. This tutorial is focused on monomer structure prediction using the Custom and Homo-oligoemrs modes. The results from Tutorial 1 will be used as inputs.

NEW: Starting from LIT-AlphaFold 1.1.0 the script inputs and some of the input files have been changed to use hydra to handle configurations, and structured .in.yaml file have replaced the unstructured .in input files.

Script parameters

Regardless of selected mode run_multimer_jobs.py always takes the same arguments.

python $LITAF/run_multimer_jobs.py \
output_path=monomer_structure \
monomer_objects_dir=[../tutorial_1_2/protein_features_mmseqs2] \
input_file=monomer_simple.in.yaml \

Arguments:

• output_path, the path to the folder where the generated structures will be saved in
• monomer_objects_dir, the paths to the folders containing the monomer .pkl files
• input_file, the file containingthe information ragarding the monomer or multimer to predict

Monomer prediction using custom

To perform monomer calculations it is necessary to write an input file, as in the example monomer_simple.in.yaml. The --- are used to separate different entries, and it is necessary to place a - before each protein name.

---
- CXCR4
---
- CXCL12

python $LITAF/run_multimer_jobs.py \
output_path=monomer_structure \
monomer_objects_dir=[../tutorial_1_2/protein_features_mmseqs2] \
input_file=[monomer_simple.in.yaml] \

The script will create in the directory monomer_structure two folders called CXCR4, and CXCL12.

Monomer prediction using homo-oligomer

Using Homo-oligomers the input file can be written by indicating the monomer object and 1 for the stochiometry

---
{monomer: CXCR4; n_units: 1}
---
{monomer: CXCL12; n_units: 1}

python $LITAF/run_multimer_jobs.py \
mode=homo-oligomer \
output_path=monomer_structure \
monomer_objects_dir=[../tutorial_1_2/protein_features_mmseqs2] \
input_file=[monomer_simple.in.yaml] \

The script will create in the directory monomer_structure two folders called CXCR4, and CXCL12.

Conclusion

In this tutorial you have learned how to run simple monomer predictions using LIT-AF.