VoxSurf: a Voxelized macromolecular Surface calculation program

摘要

We introduce VoxSurf, a Voxelized macromolecular Surface calculation program, which can produce discrete representations of molecules at very high resolutions. By employing compact data-structures and implementing a spatial slicing protocol, the proposed tool can calculate the three main molecular surfaces at high resolutions even when the available memory is limited. The generation of the Solvent Excluded surface is achieved by adopting an approximate Euclidean Distance Transform algorithm based on a data-structure called Hierarchical Queue. We show that the distance map values need to be calculated only for a small subset of the overall voxels representing the macromolecule by exploiting the geometrical relationship between the Solvent Excluded and the Solvent Accessible surfaces. A parallel implementation of the slicing procedure is also proposed and discussed.