The CX and DPX web-based servers at http://pongor.itk.ppke.hu/bioinfoservices are dedicated to the analysis of protein 3D structures submitted by the users as Protein Data Bank (PDB) files. CX computes an atomic protrusion index, cx that makes it possible to highlight the protruding atoms within a protein 3D structure. DPX calculates a depth index, dpx for buried atoms, and allows one to visualize the distribution of buried residues. CX and DPX visualize 3D structures colored according to the calculated indices and return PDB files that can be visualized using standard programs. A combined server site, the Protein Core Workbench allows visualization of dpx, cx, solvent-accessible area as well as the number of atomic contacts as 3D plots and 1D sequence plots. Online visualization of the 3D structures and 1D sequence plots are available in all three servers. Mirror sites are available at http://hydra.icgeb.trieste.it/protein/ .
Keywords: Atomic contact numbers; Atomic depth index; Protein core; Protrusion index; Solvent-accessible surface area.