David Koes edited subsection_Shape_Constraints_Since_we__.tex  over 8 years ago

Commit id: 0426fe37ee72faec97739c377170122f2d84ce24

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A \textit{maximum shape constraint} sets a strict upper bound on the volumetric shape of a target shape. Every voxel of the target shape must be contained within the maximum shape constraint. The maximum shape can be used to constrain the total volume of the target shape and prevent the target shape from overlapping undesirable areas, such as space filled by a receptor.   Shape constraints are distinct from shape similarity. Unlike shape similarity, which produces a continuous ranking of similarity with respect to a query shape, shape constraints are binary filters: a shape either matches the constraints or does not.  The structure of a  receptor-ligand complexes complex  provide a natural starting point for the development of shape constraints. The inverse of the receptor shape provides a starting point for defining a maximum shape constraint. The constraint can be expanded within the binding site as needed to incorporate tolerance for small steric clashes and receptor flexibility while the shape can be shrunk to avoid excessive exposure of the target ligand to solvent. For visualization purposes weusually  display the \textit{inverse} of the maximum shape, which corresponds to the region of space the desired shape is excluded from, to more clearly visualize the minimum shape, which is, by definition, fully subsumed in the maximum shape. Similarily, the ligand shape can be used to develop a minimum shape constraint. However, constructing a minimum shape constraint directly from the ligand shape, even if the shape is shrunk or skeletonized, results in a highly specific shape query that may be limited in its ability to retrieve novel chemical scaffolds.