Finding and filling protein cavities using cellular logic operations

Abstract

A method for solid-filling protein cavities is presented. The method uses a pattern-recognition technique based on cellular logic operations to distinguish between convex and concave regions of a protein. In doing this it solid fills protein cavities and automatically defines a boundary between cavity and exterior free space. The operations used to fill the cavities also can be used to process the filler to filter out small-scale features. So far the main use of the method has been in visualizing protein active sites for docking. The method can be used to find cavities of a given size range and could be used to find novel protein binding sites.