Protein structures are an ensemble of atoms determined experimentally mostly by X-ray crystallography or Nuclear Magnetic Resonance. Studying 3D protein structures is a key point for better understanding protein function at a molecular level. To do so, a set of accurate tools was implemented in a program, reffered to as VLDP (Voronoi Laguerre Delaunay Protein). Based on the reliable method of Voronoi-Laguerre tessellations, VLDP program gives amongst others the following data: (i) Amino acid volumes evaluated with high precision, as confirmed by good correlations with experimental data [1,3]. (ii) A novel definition of inter-residue contacts within the given protein [2,3]. (iii) A measure of the residue exposure to solvent that significantly improves the standard notion of accessibility in some cases [1,3]. Finally, VLDP is a powerful geometric-topological tool for analysing protein structures and their surroundings (for example, water network), but it could be extended to a wider scope.