Efficiently Mining Recurrent Substructures from Protein Three-Dimensional Structure Graphs

Mining Spatial Motifs from Protein Structure Graphs

Finding recurring structural features among proteins three-dimensional (3D) structures is an important problem in bioinformatics. In this paper we apply a novel subgraph mining algorithm to three related graph representations of the sequence and proximity characteristics of a protein’s amino acid residues. The subgraph mining algorithm is used to discover spatial motifs that can be used to disc...

Modeling Protein Structure Features from Three Dimensional Cryo-EM Images

Secondary structure of protein, such as α-helix and βsheet, is the general three-dimensional (3D) form of local segments. It can be identified from the 3D electron cryomicroscopy (cryo-EM) density images at medium resolutions (~5-10Å). A detected β-sheet can be represented by either the voxels of β-sheet density or by many piecewise polygons to compose a rough surface. However, none of these is...

Three-dimensional Straight Skeletons from Bisector Graphs

A straight skeleton of a polygon or of a polytope is a piecewise linear skeletal structure that partitions the underlying object by means of a self-parallel shrinking process. We propose a method for constructing different straight skeletons for a given nonconvex polytope Q in 3-space. The approach is based on so-called bisector graphs on the sphere, and allows for generating straight skeletons...

Prediction of Protein Three-Dimensional Structure

Perception of three-dimensional structure from motion.

The ability to perceive the 3-D shape of objects solely from motion cues is referred to as structure-from-motion perception. Recent experiments indicate how this remarkable perceptual attribute is computed by the brains of primates. This computation proceeds in at least two stages, one in which motion measurements are made and another in which moving surfaces are reconstructed. The middle tempo...