Improving classification of correct and incorrect protein–protein docking models by augmenting the training set

Abstract

Abstract Motivation Protein–protein interactions drive many relevant biological events, such as infection, replication and recognition. To control or engineer such events, we need to access the molecular details of the interaction provided by experimental 3D structures. However, such experiments take time and are expensive; moreover, the current technology cannot keep up with the high discovery rate of new interactions. Computational modeling, like protein–protein docking, can help to fill this gap by generating docking poses. Protein–protein docking generally consists of two parts, sampling and scoring. The sampling is an exhaustive search of the tridimensional space. The caveat of the sampling is that it generates a large number of incorrect poses, producing a highly unbalanced dataset. This limits the utility of the data to train machine learning classifiers. Results Using weak supervision, we developed a data augmentation method that we named hAIkal. Using hAIkal, we increased the labeled training data to train several algorithms. We trained and obtained different classifiers; the best classifier has 81% accuracy and 0.51 Matthews’ correlation coefficient on the test set, surpassing the state-of-the-art scoring functions. Availability and implementation Docking models from Benchmark 5 are available at https://doi.org/10.5281/zenodo.4012018. Processed tabular data are available at https://repository.kaust.edu.sa/handle/10754/666961. Google colab is available at https://colab.research.google.com/drive/1vbVrJcQSf6\_C3jOAmZzgQbTpuJ5zC1RP?usp=sharing Supplementary information Supplementary data are available at Bioinformatics Advances online.