- sfcheck - run CCP4Online sfcheck
- CASTp - webserver for identification and measurements of surface accessible pockets as well as interior
- DIMPLOT - Interactions between monomers of a dimer
- FADE and PADRE - Shape and Complementarity Server
- GRASP - Calculate electrostatic potential
- LIGPLOT - Interactions around a ligand of piece of structure. There is also LigPlot+ at http://www.ebi.ac.uk/thornton-srv/software/LigPlus/; the PDBsum server internally runs ligplot and returns pdf files; non-released PDB files can be handled using the "generate" option in the left panel
- NACCESS - Surface area calculaitons, per residue, or atom
- NCONT - (ccp4) analyses contacts between subsets of atoms in a PDB file
- Protein-Protein Interaction Server - stats on your chain interfaces and to obtain surface calculations
- PARVATI - anisotropic displacement parameters statistics
- SURFACE and AREAIMOL - (ccp4) -surface programs
- VOIDOO - look for interior cavities
- VADAR - (Volume, Area, Dihedral Angle Reporter)