Fig. 1
From: A fragment based method for modeling of protein segments into cryo-EM density maps
Workflow of FragFit. As input (top), (1) a PDB structure, (2) the stem atoms of residues flanking the queried segment, (3) the amino acid sequence of the queried segment and (4) the cryo-EM density map with (5) its resolution must be provided. a Sequence similarity between fragment and queried segment and matching of geometric fingerprints (Additional file 1: Figure S2) are used as evaluation criteria for FragSearch. b Cryo-EM density maps are preprocessed to minimize calculation time and to reduce false positive predictions. For that purpose, a minimal box limited to the maximum density of the missing segment is extracted and occupied densities are deleted. c Suitable fragments identified by FragSearch are re-scored by the Pearson cross-correlation coefficient between simulated and experimentally determined cryo-EM density maps, which selects for the best fitting fragments. All steps are presented in more detail in Additional file 1: Figure S6