title: 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.
authors.affiliation: Department of Industrial Engineering, Hanyang University, 17 Haengdang-dong, Seongdong-gu, Seoul 133-791, South Korea. dskim@hanyang.ac.kr
authors.forename: Deok-Soo
authors.initials: DS
authors.lastname: Kim
authors.forename: Chung-In
authors.initials: CI
authors.lastname: Won
authors.forename: Jong
authors.initials: J
authors.lastname: Bhak
mesh_terms: D008958:Models, Molecular; D011506:Proteins / Q000737:chemistry*; D013499:Surface Properties; D009626:Terminology as Topic
chemical_list: D011506:Proteins