Fig. 5: Local confidence estimation of the built models.
From: Automated detection and de novo structure modeling of nucleic acids from cryo-EM maps
a Local confidence score is defined as the predicted atom probability at the C4' position. b The nucleotide displacements versus their local confidence scores for n = 8523 C4' atoms that represent the corresponding nucleotides on the main test set of 50 maps. The thick dots indicate the means and error bars/whiskers indicate ± 1.0 standard deviations. c The distribution (Fill Area, left y-axis) and accumulated percentages (Line+Symbol, right y-axis) of local confidences for the built nucleotides in helical and non-helical regions. d Box plots of local confidence scores for n = 5758 helical and n = 2765 non-helical nucleotides. The box plots indicate the means (cross), medians (median-line), first and third quartiles (bounds of boxes), and ± 1.0 standard deviations (whiskers). Mean values are marked near the box. e Examples of the EM2NA-built models colored by local confidence scores. The superimposed PDB structure is colored in green. From left to right are EMD-23600, PDB 7LYS, CasPhi-2 (Cas12j) bound to crRNA and DNA; EMD-23721, PDB 7M9A, ADP-AlF3 bound TnsC structure from ShCAST system; EMD-34832, PDB 8HJ4, anti-CRISPR protein AcrIIC5 bound to Nme1Cas9-sgRNA; and EMD-26856, PDB 7UXA, human tRNA Splicing Endonuclease Complex bound to pre-tRNA-ARG. As indicated in dashed rectangles, non-helical nucleotides tend to be built with lower confidences. Source data are provided as a Source Data file.
