A Proposal for the Revision of Molecular Boundary Typology

Abstract

Molecular shape is essential in understanding molecular function, and understanding molecular shape requires definition of molecular boundaries. In this paper, we review the conceptual evolution of three molecular boundary types: the van der Waals surface, the Connolly surface, and the Lee-Richards (accessible) surface. Then, we point out the confusion among the names of these surfaces existing in the literature. Since it is desirable to have a well- defined terminology in a discipline, we propose the standard names of the three molecular boundary types and their corresponding volumes in order to maximize consistency among researchers, respect the first individual who defined or computed a surface type, and promote collaboration between biologists and geometers.

Key words:

• van der Waals surface
• Connolly surface
• Lee-Richards surface
• Molecular surface
• Solvent-accessible surface
• Solvent-excluded surface
• Blended surface
• Offset surface