Fig. 1 | Nature Communications

Fig. 1

From: De novo main-chain modeling for EM maps using MAINMAST

Fig. 1

Flowchart of MAINMAST. Steps of the MAINMAST algorithm is illustrated with a modeling example for an EM density map of structural protein 5 of cytoplasmic polyhedrosis virus solved at a 2.9 Å resolution (EMD-6374). First, points with high local density are identified with the mean shift algorithm. The color scale of the points indicate density, blue to orange for low to high density. Identified local dense points are connected by minimum spanning tree (MST) (cyan). Using tabu-search, the initial MST is refined and a few thousands of alternative MSTs are generated. For each MST, the amino acid sequence of the query protein is mapped on the longest path in the tree by matching the volume of amino acids to the density of the local dense points (threading). Cα models from each MST are ranked with the density–volume matching (threading) score. In the third panel on the right, the blue chain represents a Cα model and the structure in magenta is the native structure. Selected Cα models are refined with a sequential application of PULCHRA and MDFF to obtain final full-atom models (turquoise)

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