Graphics Native Approach to Identifying Surface Atoms of Macromolecules

Classification of “surface atoms” or “interior atoms” of proteins or other macromolecules is significant for many biochemical tasks, particularly for molecular docking. We present a simple and easy-to-implement algorithm for identifying surface atoms of macromolecules from interior atoms. Unlike existing methods that are based on geometry computations, our approach takes the advantage of graphics hardware, and most of the computations are fulfilled with graphics processing unit (GPU). The algorithm can be easily incorporated within visualization applications for macromolecules to enable the removal of interior atoms from a macromolecular structure, thus simplifying the graphics display and manipulation.