Molecular shape analysis based upon the morse-smale complex and the connolly function

Docking is the process by which two or several molecules form a complex. Docking involves the geometry of the molecular surfaces, as well as chemical and energetical considerations. In the mid-eighties, Connolly proposed a docking algorithm matching surface knobs with surface depressions. Knobs and depressions refer to the extrema of the Connolly function, which is defined as follows. Given a surface M bounding a three-dimensional domain X, and a sphere S centered at a point p of M, the Connolly function is equal to the solid angle of the portion of S containing within X.We recast the notions of knobs and depressions in the framework of Morse theory for functions defined over two-dimensiona…