from https://bioinformatictools.wordpress.com/tag/model-validation/:

"Verifying your modeled protein with online servers:

Stuctural Analysis and Verification Server (SAVS): http://nihserver.mbi.ucla.edu/SAVES/ SAVS uses following servers to check the quality of the protein structures: Procheck: Checks the stereochemical quality of a protein structure by analyzing residue-by-residue geometry and overall structure geometry. [Reference] 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. [Reference] 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. [Reference] Verify3D: Determines the compatibility of an atomic model (3D) with its own amino acid sequence (1D) by assigned a structural class based on its location and environment (alpha, beta, loop, polar, nonpolar etc) and comparing the results to good structures. [Reference] Prove: Calculates the volumes of atoms in macromolecules using an algorithm which treats the atoms like hard spheres and calculates a statistical Z-score deviation for the model from highly resolved (2.0 Å or better) and refined (R-factor of 0.2 or better) PDB-deposited structures. [Reference]

COLORADO-3D: http://asia2.genesilico.pl/colorado3d/ COLORADO-3D is a www-tool that greatly facilitates the visual analysis of various features in three-dimensional protein structures, directly at the level of the protein structure, with the aid of commonly used viewers such as RASMOL or SWISSPDBVIEWER. Among the features most important for the structural biologist that our server allows to visualize in color are potential errors in protein structure (detected by ANOLEA, PROSA, PROVE,VERIFY3D), regions buried in the protein core and inaccessible to the solvent, and regions of high or low sequence conservation (e.g. detected by RATE4SITE). In particular COLORADO3D may serve to visualize the results of assessment of the protein structure’s quality at various stages of the model building and refinement (both in the case of experimental structure determination and homology modeling)."