Description of Protein-DNA Complexes in Terms of Electron-Density Topological Features

This paper presents a computer-modelling approach for the generation of low-resolution representations of two protein-DNA complexes, NF-κB and HIF-1. The representation is obtained by topological analysis of electron-density maps at 2.85 A crystallographic resolution, which leads to a set containing a limited number of critical points (CP). Analyses of the structure and properties of the CP graphs (density at peak position, volume and ellipticity), as well as comparisons with other reduced representations, are performed in order to assess the usefulness of such representations in molecular-docking applications at medium resolution.