TABLE 2.
Evaluation of detected helices and β-sheets from DeepSSETracer 0.1 and Emap2sec+ using 28 cryo-EM component maps. From the left to right: the EMDB ID, PDB ID, chain ID with the resolution of the cryo-EM map in parentheses, the number of Cα atoms in the STRIDE-annotated PDB file for H: helix, S: β-sheet, T: total of the chain, voxel-level of F1-scores for helix detection (H-V) and β-sheet detection (S-V), residue-level F1-scores for helix detection (H-R) and β-sheet detection (S-R) for DeepSSETracer 0.1 and Emap2sec+ respectively. NA: zero number of residues of the corresponding class in the atomic structure and undefined precision or recall.
| EMDB_PDB_Chain (resolution Å) | Cα(H/S/T) | DeepSSETracer 0.1 | Emap2sec+ | ||||
|---|---|---|---|---|---|---|---|
| H-V | S-V | H-R | S-R | H-R | S-R | ||
| 1798_4v5m_AE (7.80) | 42/58/150 | 0.64 | 0.54 | 0.85 | 0.66 | 0.86 | 0.59 |
| 2994_5a21_G (7.20) | 37/21/133 | 0.38 | 0.37 | 0.37 | 0.41 | 0.43 | 0.31 |
| 3206_5fl2_K (6.20) | 12/47/106 | 0.62 | 0.62 | 0.8 | 0.78 | 0.25 | 0 |
| 3491_5mdx_H (5.30) | 33/0/42 | 0.69 | NA | 0.84 | NA | 0.79 | NA |
| 3850_5oqm_4 (5.80) | 128/49/297 | 0.58 | 0.59 | 0.71 | 0.73 | 0.73 | 0.67 |
| 3850_5oqm_g (5.80) | 81/0/85 | 0.74 | NA | 0.98 | NA | 0.98 | NA |
| 3948_6esg_B (5.40) | 51/0/78 | 0.70 | NA | 0.81 | NA | 0.97 | NA |
| 4041_5ldx_I (5.60) | 48/19/176 | 0.51 | 0.39 | 0.69 | 0.56 | 0.61 | 0.43 |
| 4078_5lms_D (5.10) | 86/18/208 | 0.52 | 0.32 | 0.63 | 0.38 | 0.65 | 0.53 |
| 4141_5m1s_B (6.70) | 81/158/366 | 0.56 | 0.55 | 0.72 | 0.73 | 0.68 | 0.69 |
| 4182_6f42_G (5.50) | 16/66/180 | 0.55 | 0.46 | 0.70 | 0.71 | 0.75 | 0.57 |
| 5942_3j6x_25 (6.10) | 25/5/70 | 0.18 | 0.15 | 0.14 | 0.27 | 0.71 | 0 |
| 5943_3j6y_80 (6.10) | 12/8/52 | 0.44 | 0 | 0.61 | 0 | 0.51 | 0 |
| 6149_3j8g_W (5.00) | 19/48/94 | 0 | 0.59 | 0 | 0.77 | 0.59 | 0 |
| 6446_3jbi_V (8.50) | 116/0/131 | 0.72 | NA | 0.87 | NA | 0.92 | NA |
| 6456_3jbn_AL (6.70) | 89/8/211 | 0.57 | 0.18 | 0.75 | 0.29 | 0.83 | 0 |
| 6810_5y5x_H (5.00) | 38/10/100 | 0.11 | 0.47 | 0.14 | 0.60 | 0.58 | 0 |
| 7454_6d84_S (6.72) | 65/34/142 | 0.49 | 0.51 | 0.55 | 0.64 | 0.66 | 0.27 |
| 8016_5gar_O (6.40) | 65/0/80 | 0.26 | NA | 0.24 | NA | 0.7 | NA |
| 8128_5j7y_K (6.70) | 71/0/93 | 0.72 | NA | 0.89 | NA | 0.92 | NA |
| 8129_5j8k_AA (7.80) | 187/60/446 | 0.62 | 0.48 | 0.75 | 0.63 | 0.73 | 0.23 |
| 8129_5j8k_D (7.80) | 170/41/384 | 0.58 | 0.29 | 0.69 | 0.38 | 0.73 | 0 |
| 8130_5j4z_B (5.80) | 63/9/154 | 0.73 | 0.28 | 0.88 | 0.33 | 0.79 | 0.44 |
| 8135_5iya_E (5.40) | 88/44/210 | 0.64 | 0.52 | 0.79 | 0.67 | 0.79 | 0.68 |
| 8357_5t4o_L (6.90) | 106/0/160 | 0.67 | NA | 0.82 | NA | 0.82 | NA |
| 8518_5u8s_A (6.10) | 114/13/208 | 0.69 | 0.54 | 0.86 | 0.68 | 0.88 | 0.33 |
| 8693_5viy_A (6.20) | 68/0/133 | 0.66 | NA | 0.83 | NA | 0.75 | NA |
| 9534_5gpn_Ae (5.40) | 59/0/88 | 0.60 | NA | 0.75 | NA | 0.83 | NA |
| Weighted Average | 1970/716/4,577 | 0.59 | 0.49 | 0.72 | 0.65 | 0.77 | 0.42 |
Weighted average: averaged F1 scores of all 28 test cases, weighted by the ratio of the number of residues of the class in each case and the total number of residues in the test set.