An efficient algorithm for computing the area of a molecular surface using β-complex

Abstract

It is well known that the structure of a protein mostly determines the function of a protein. Hence, the structure of a protein is very important for studying the function of a protein. A molecular surface of a protein is one of the important structures for a protein. The area of a molecular surface is critically related with protein docking and protein folding through solvation energy. This paper presents an algorithm for computing the area of a molecular surface precisely and efficiently based on a β-complex. Given a β-complex of a protein, the algorithm can compute the area of a molecular surface in O(n) time in the worst case where n is the number of atoms in the protein.