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. Author manuscript; available in PMC: 2022 Nov 14.
Published in final edited form as: Robotica. 2016 May 19;34(8):1777–1790. doi: 10.1017/s0263574716000242

Figure 1. Secondary structure traces, skeleton, and topology.

Figure 1

(A) The 3D image (gray) was simulated to 10 Å resolution using atomic structure 3PBA from the Protein Data Bank (PDB) and EMAN software.73 Secondary structure traces (red sticks: α-traces; purple: β-strands) were detected using SSETracer55 and StrandTwister39 and viewed using Chimera.76 See the detected β-traces (blue) in (B) for clear viewing. Only those at the front of the structure are labeled. Arrows: the direction of the protein sequence; (B) The skeleton (yellow) derived from the image is superimposed on the traces of helices (red) and β-strands (blue). (C) The amino acid sequence of protein 3PBA is annotated with secondary structures using red rectangles (helices) and blue triangles (β-strands). The two smaller triangles S3 and S7 were not detected in the image. Loops longer than two amino acids are indicated using “…”.