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Table 6 Predicted and true residue type for the wild type and mutant structures at the variant sites

From: 3D deep convolutional neural networks for amino acid environment similarity analysis

  1. Distinct prediction patterns can be observed between the destabilizing and neutral variants. For the destabilizing variants, our network makes correct predictions with very high confidence on the wild type microenvironments and the predictions on the mutant microenvironments often resemble the true wild type residues, as highlighted in orange. On the other hand, predictions on wild type environment vary significantly. Predictions on mutant microenvironment do not resemble the wild type amino acid, but are rather more similar to the mutant amino acid type, as highlighted in blue. For some cases, predictions of the wild type environment even match exactly to the mutant residues, as highlighted in yellow. These findings suggest that destabilizing mutations happens in microenvironments where the wild type amino acid are strongly preferred while the neutral ones tend to be observed when amino acids other than the wild type are tolerated or even preferred