DeepTracer: Predicting Backbone Atomic Structure from High Resolution Cryo-EM Density Maps of Protein Complexes

Jonas Pfab; Dong Si

We measure the accuracy of a predicted protein structure by comparing it to its corresponding solved structure using the following metrics. First, the root-mean-square deviation (RMSD) value describes the average distance between atoms of the predicted and solved protein structure. This gives us an idea how close the predicted atoms are to their correct counter parts. However, this does not give us any information about the percentage of atoms that we have correctly identified. For this purpose, we calculate the coverage value, which expresses the percentage of atoms in the solved structure that lay within 3Å of a predicted atom. Finally, we evaluate the false-positive percentage which is the number of atoms that were predicted further than 3Å from any atom in the solved structure, divided by the total number of predicted atoms. In addition to the metrics that we use to compare the other methods to the DeepTracer, we also calculate the secondary structure and amino acid type accuracy. We cannot evaluate these for the other methods as they utilize the U-Net confidence maps rather than the predicted protein structure. The secondary structure accuracy is defined as the percentage of atoms from the solved structure whose secondary structure type equals the one predicted by the U-Net for its location. The amino acid type accuracy is calculated in the same way. In Table 1 , we can see the test results for all 30 density maps. 2 Number of Cα atoms in the solved protein structure 3 Percentage of atoms that were predicted further than 3A away from any atoms in the solved structure 4 Percentage of atoms from the solved structure that lay within 1A of a predicted atom 5 Percentage of atoms from the solved structure for which the U-Net correctly predicted the secondary structure 6 Percentage of atoms from the solved structure for which the U-Net correctly predicted the amino acid type (missing entries indicate that the solved structure did not contain amino acid type information)