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 ...