Improved Assessment of Globularity of Protein Structures and the Ellipsoid Profile of the Biological Assemblies from the PDB.

ABSTRACT: In this paper, we present an update to the ellipsoid profile algorithm (EP), a simple technique for the measurement of the globularity of protein structures without the calculation of molecular surfaces. The globularity property is understood in this context as the ability of the molecule to fill a minimum volume enclosing ellipsoid (MVEE) that approximates its assumed globular shape. The more of the interior of this ellipsoid is occupied by the atoms of the protein, the better are its globularity metrics. These metrics are derived from the comparison of the volume of the voxelized representation of the atoms and the volume of all voxels that can fit inside that ellipsoid (a uniform unit Å cube lattice). The so-called ellipsoid profile shows how the globularity changes with the distance fr

SUBMITTER: Banach M 

PROVIDER: S-EPMC9953691 | biostudies-literature | 2023 Feb

REPOSITORIES: biostudies-literature