ProTailor: a Parallel Operator for Extremely Fast Shape Analysis in Bioinformatics Applications

The geometric shape of molecular surfaces strongly
influences the docking processes where, although electrostatic,
hydrophobic and van der Waals interactions affect greatly the
binding affinity of the molecules, shape complementarity is a
necessary condition. The vast majority of molecular docking
algorithms uses a brute force enumeration of the
transformation space, which requires extremely long running
times. Few other methods use local shape feature matching to
reduce the search to those relative positions which satisfy
geometric constraints.
Based on a shape analysis tool developed in Computer
Graphics, in this paper we introduce ProTailor, a parallel
algorithm for efficient multi-scale detection of morphological
features on molecular surfaces. Thanks to an almost linear
speed-up, we show how ProTailor is well suited to efficiently
identify salient features like cavities and depressions, saddle
areas or bridges. Feature identification may serve as a
powerful tool to automatically locate potential binding sites or
as a pre-processing step for efficient shape complementarity
assessment in docking prediction.