Detection of cave pockets in large molecules: Spaces into which internal probes can enter, but external probes from outside cannot.

ABSTRACT: Geometric features of macromolecular shapes are important for binding with other molecules. Kawabata, T. and Go, N. (2007) defined a pocket as a space into which a small probe can enter, but a large probe cannot. In 2010, mathematical morphology (MM) was introduced to provide a more rigorous definition, and the program GHECOM was developed using the grid-based representation of molecules. This method was simple, but effective in finding the binding sites of small compounds on protein surfaces. Recently, many 3D structures of large macromolecules have been determined to contain large internal hollow spaces. Identification and size estimation of these spaces is important for characterizing their function and stability. Therefore, we employ the MM definition of pocket proposed by Manak, M. (2

SUBMITTER: Kawabata T 

PROVIDER: S-EPMC6975925 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature