A method for the quantitative evaluation of structural similarity between protein pairs is developed that makes use of a Delaunay-based topological mapping. The result of the mapping is a three-dimensional array which is representative of the global structural topology and whose elements can be used to construe an integral scoring scheme. This scoring scheme was tested for its dependence on the...

Biomolecular structure comparison not only reveals evolutionary relationships, but also sheds light on biological functional properties. However, traditional definitions of structure or sequence similarity always involve superposition or alignment and are computationally inefficient. In this paper, I propose a new method called persistent similarity, which is based on a newly-invented method in...

This paper derives and compares two strategies for minimizing topological constraints in a query expressed by a visual example: (1) elimination of topological relations that are implied uniquely by composition and (2) restriction to topological relations that relate near-neighbor objects, as determined by a Delaunay triangulation. In both cases, the query processing approach is to solve a const...

Based on the 9-intersection for binary topological relations, two models of conceptual neighborhoods among topological relations between a line and a region are developed. The snapshot model derives the neighborhoods by comparing pairs of topological relations and selects neighbors based on least noticeable differences, whereas the smooth-transition model develops neighborhoods based on the kno...