Analysis of algorithms on extracting molecular surface atoms

In this paper, we revise an algorithm named PSAGA that is used to extract the molecular surface atoms according to the molecule's 3D geometric characteristic. The PSAGA algorithm has some problems because the critical state is not exact, so we improve this algorithm by adjusting the critical state. Besides, a new extraction algorithm is proposed. The new algorithm uses a probe sphere contacting with the atoms to judge which is the surface atom. Experiments show that the new extraction algorithm is more accurate. And we also analyze the three algorithms according to the accuracy and the execution time.