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A proposal for the revision of molecular boundary typology
Deok-Soo Kim1, Chung-In Won, Jong Bhak
1Department of Industrial Engineering, Hanyang University, 17 Haengdang-dong, Seongdong-gu, Seoul 133-791, South Korea. dskim@hanyang.ac.kr
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.
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