Extended Data Fig. 4: Grid level detection accuracy (recall) of 8 structural classes.
From: CryoREAD: de novo structure modeling for nucleic acids in cryo-EM maps using deep learning
A grid was assigned with a structure class that is closer than 2 Å to the grid. If there were multiple different structures that were within 2 Å, the closer one was assigned to the grid. A detection by deep network for a grid was considered as correct if the probability of the correct structure class has a value over 0.5. pho, phosphate. Results of the stage 1 and stage 2 networks are shown. The statistics are calculated over n = 68 independent experimental EM maps, with each points values derived from Supplementary Table 2. For stage 1, the values of minima, maxima, center, bounds of box and whiskers of different categories in order: Sugar(0.333,0.893,0.729,0.601/0.804,0.333/0.893), Phos(0.138,0.849,0.656,0.463/0.754,0.138/0.849), Base(0.380,0.947,0.836,0.772/0.889,0.669/0.947), Protein(0.349,0.929,0.808,0.763/0.879,0.621/0.929), A-Base(0.034,0.890,0.549,0.362/0.746,0.034/0.890), U/T-Base(0.019,0.797,0.460,0.294/0.646,0.019/0.797), C-Base(0.088,0.886,0.539,0.369/0.711,0.088/0.886), G-Base(0.153,0.933,0.637,0.490/0.823,0.153/0.933), Overall(0.438,0.909,0.764,0.685/0.822,0.478/0.909). For stage 2, the values of minima, maxima, center, bounds of box and whiskers of different categories in order: Sugar(0.357,0.920,0.775,0.654/0.846,0.453/0.920), Phos(0.228,0.883,0.693,0.509/0.810,0.228/0.883), Base(0.408,0.952,0.858,0.795/0.905,0.695/0.952), Protein(0.490,0.969,0.903,0.867/0.936,0.772/0.969), A-Base(0.013,0.893,0.501,0.296/0.745,0.013/0.893), U/T-Base(0.024,0.824,0.479,0.291/0.682,0.024/0.824), C-Base(0.104,0.920,0.611,0.449/0.775,0.104/0.920), G-Base(0.237,0.951,0.737,0.609/0.858,0.237/0.951), Overall(0.492,0.952,0.827,0.756/0.878,0.577/0.952). For the moiety level accuracy, see Fig. 2 in the main text.
