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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 approach is based on the transformation of the simplex search problem in the R3 space to the orthogonal range search problem of points in another R3 space.