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Single (or Multiple) Model Protein Structure Analysis   VADAR (Volume, Area, Dihedral Angle Reporter) is a compilation of more than 15 different algorithms and programs for analyzing and assessing peptide and protein structures from their PDB coordinate data. The results have been validated through extensive comparison to published data and careful visual inspection.  The VADAR web server supports the submission of either PDB formatted files or PDB accession numbers.  VADAR produces extensive tables and high quality graphs for quantitatively and qualitatively assessing protein structures determined by X-ray crystallography, NMR spectroscopy, 3D-threading or homology modelling.     ResProx ( Res olution-by- prox y or Res(p)) is a web server that predicts the atomic resolution of NMR protein structures using only PDB coordinate data as input. More specfically, ResProx uses machine lea...

Homology model can be validated in multiple ways. Here you will find useful description on how to validate your homology model. Web-servers: UCLA-DOE LAB — SAVES : The Structure Analysis and Verification Server ( New Link ) This metaserver runs 6 programs for checking and validating protein structures during and after model refinement. PROCHECK : Checks the stereochemical quality of a protein structure by analyzing residue-by-residue geometry and overall structure geometry. WHAT_CHECK : Derived from a subset of protein verification tools from the WHATIF program (Vriend, 1990), this does extensive checking of many sterochemical parameters of the residues in the model.   ERRAT : Analyzes the statistics of non-bonded interactions between different atom types and plots the value of the error function versus position of a 9-residue sliding window, calculated by a comparison with statistics from highly refined structures.   VERIFY_3D : Determines the ...