TopFit integrates protein structure data with sequence embeddings to improve predictions of the protein fitness landscape. NBThighlight
for the correspondence between dataset naming convention used in this file and that in figures. Dataset with additional suffix “_AF” or “_NMR” indicate AF or NMR structure was used for computations. In each folder, results are saved in “.csv” with eight possible names for different tasks. “ridge.csv”, “ensemble.csv”, “evolutionary_scores.csv” are results from random train/test splits using ridge regression, ensemble regression and evolutionary scores, respectively. “unseen_ensemble.
csv” are results from train/test splits for unseen mutational sites using ensemble regression and evolutionary scores, respectively. “ridge_n_mut_1.csv”, “ensemble_n_mut_1.csv”, “evolutionary_scores_n_mut_1.csv” are results from extrapolation task that single mutations are used to predict multiple mutations for ridge regression, ensemble regression and evolutionary scores, respectively. Explanations for column name are available in “README.txt”.
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