Alpha shapes applied to molecular shape characterization exhibit novel properties compared to established shape descriptors.

ABSTRACT: Despite considerable efforts, description of molecular shape is still largely an unresolved problem. Given the importance of molecular shape in the description of spatial interactions in crystals or ligand-target complexes, this is not a satisfying state. In the current work, we propose a novel application of alpha shapes to the description of the shapes of small molecules. Alpha shapes are parametrized generalizations of the convex hull. For a specific value of alpha, the alpha shape is the geometric dual of the space-filling model of a molecule, with the parameter alpha allowing description of shape in varying degrees of detail. To date, alpha shapes have been used to find macromolecular cavities and to estimate molecular surface areas and volumes. We developed a novel methodology for co

SUBMITTER: Wilson JA 

PROVIDER: S-EPMC3158582 | biostudies-literature | 2009 Oct

REPOSITORIES: biostudies-literature