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.

Script parameters

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

python $LITAF/run_multimer_jobs.py --mode custom \
--output_path monomer_structure \
--monomer_objects_dir ../tutorial_1_2/protein_features_mmseqs2 \
--input_file monomer_simple.in \
--data_dir $AFDATA \

Arguments:

• mode, specieifes the method used for calculations
• output_path, the path to the folder where the generated structures will be saved in
• monomer_objects_dir, the path to the folders containing the monomer .pkl files
• input_file, the file containingthe information ragarding the monomer or multimer to predict
• data_dir, the path to the folder containing the databases and models' weights of AlphaFold

Monomer prediction using custom

To perform monomer calculations it is necessary to write an input file, as in the example monomer_simple.in.

CXCR4
CXCL12

python $LITAF/run_multimer_jobs.py --mode custom \
--output_path monomer_structure \
--monomer_objects_dir ../tutorial_1_2/protein_features_mmseqs2 \
--input_file monomer_simple.in \
--data_dir $AFDATA \

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 in two ways:

• Indicating the monomer object and 1 for the stochiometry

CXCR4;1
CXCL12;1

• Indicating just the monomer object, the script will by default consider it as a monomer, as in the example monomer_simple.in.

CXCR4
CXCL12

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 \
--data_dir $AFDATA \

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.