Predicting Antibody Affinity Changes upon Mutations by Combining Multiple Predictors

Required Packages

The following is the list of required packeages and programs, as well as the version on which it was tested (in parenthesis).

• Python (3.7.2)
• numpy (1.16.3)
• pandas (0.24.2)
• scikit-learn (0.21.2)
• statistics (1.0.3.5)

SiPMAB

python corr_run.py ../Input/ddG.csv [SEED] # calculate peason's correlation each seed
python analysis.py # calculate mean and SE of the peason's correlation
python fi_analysis.py # calculate feature importance

Independent data

python pred_holdout.py ../Input/test_2bdn_3bdy.csv ${SEED}

Reference

Kurumida Y, Saito Y, Kameda T. Predicting antibody affinity changes upon mutations by combining multiple predictors. Sci Rep. 2020 Nov 11;10(1):19533. doi: 10.1038/s41598-020-76369-8.