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Protein-ligand docking is to predict the location and orientation of a ligand with respect to a protein within its binding site, and has been known to be essential for the development of new drugs. The protein-ligand docking problem is usually formulated as an energy minimization problem to identify the docked conformation of the ligand. A ligand usually docks around a depressed region, called a pocket,...
Given a quasi-triangulation, the dual structure of the Voronoi diagram of a molecule, querying its simplexes of a particular bounding state for the spherical probe of a given radius occurs frequently. The β-complex and the β-shape are such examples with various applications for reasoning the spatial structure of molecules. While such simplexes can be found by linearly scanning all simplexes in the...
Molecular shape is one of the most critical factors that determine molecular function. To properly understand the function of a molecule, it is necessary to explore its geometric properties more effectively and efficiently in addition to its physicochemical properties. Due to the complexity of the problems in biomolecular structure, in-silico approach is inevitable for many cases and is becoming more...
Given a quasi-triangulation of a molecule, searching the simplexes of a particular bounding state for the spherical probe of a given radius occurs frequently. While such simplexes can be found by linearly scanning all simplexes in the quasi-triangulation, it is desirable to do the search faster. This paper presents an algorithm for searching simplexes quickly using the kd-tree data structure. The...
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