Model Evaluation

From CCP4 wiki
  • 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)