A new method for mapping macromolecular topography.
A new method, using circular variance, is introduced for mapping macromolecular topography. Circular variance, generally used to measures angular spread, can be used to characterize of molecular structures based on a simple idea. It will be shown that the circular variance of vectors drawn from some origin to a set of points is well correlated with the degree to which that origin is inside/outside the chosen points. In addition, it has continuous derivatives that are also easy to compute. This concept will be shown to be useful for: (i) distinguishing between atoms near the surface of a macromolecule and those in either the deep interior or remote exterior; (ii) identifying invaginations (even shallow ones); and (iii) detecting linker regions that interconnect two domains.
Mezei
Mihaly
M
Department of Physiology and Biophysics, Mount Sinai School of Medicine, NYU, NY 10029, USA. mezei@inka.mssm.edu
D000465:Algorithms; D001436:Bacteriorhodopsins / Q000737:chemistry; D003198:Computer Simulation; D003459:Crystallins / Q000737:chemistry; D008433:Mathematics; D008958:Models, Molecular; D038222:gamma-Crystallins
D003459:Crystallins; C107738:crystallin, gammaB; D038222:gamma-Crystallins; D001436:Bacteriorhodopsins