Estimating Lower Bounds on the Length of Protein Polymer Chain Segments using Robot Motion Planning

Finding the 3D structure a protein will assume given only its amino acid sequence remains largely an open question in bioinformatics. New developments have incorporated 3D images–”density maps”–of molecules from electron microscopy, but this presents its own problems. We seek to measure the lengths of segments of protein polymer chains associated with specific regions of the density map. We briefly discuss past efforts, and introduce an analog to robot motion planning as a novel approach. We will show this new approach’s superiority through complexity analysis, and present some experimental results in the 2D case, leaving the 3D case to future work. Keywords-simplification; bounded; skeleton; shortest-path; graph