ANALYTICAL SHAPE COMPUTATION OF MACROMOLECULES - I - MOLECULAR AREA AND VOLUME THROUGH ALPHA-SHAPE

The size and shape of macromolecules such as proteins and nucleic acid s play an important role in their functions. Prior efforts to quantify these properties have been based on various discretization or tessell ation procedures involving analytical or numerical computations. In th is article, we present an analytically exact method for computing the metric properties of macromolecules based on the alpha shape theory. T his method uses the duality between alpha complex and the weighted Vor onoi decomposition of a molecule. We describe the intuitive ideas and concepts behind the alpha shape theory and the algorithm for computing areas and volumes of macromolecules. We apply our method to compute a reas and volumes of a number of protein systems. We also discuss sever al difficulties commonly encountered in molecular shape computations a nd outline methods to overcome these problems. (C) 1998 Wiley-Liss, In c.