A proposal for the revision of molecular boundary typology.
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.
Kim
Deok-Soo
DS
Department of Industrial Engineering, Hanyang University, 17 Haengdang-dong, Seongdong-gu, Seoul 133-791, South Korea. dskim@hanyang.ac.kr
Won
Chung-In
CI
Bhak
Jong
J
D008958:Models, Molecular; D011506:Proteins / Q000737:chemistry*; D013499:Surface Properties; D009626:Terminology as Topic
D011506:Proteins