Comparison of three different protein structure modeling protocols for modeling TPIs. The RMSD of atoms of charged side chains is plotted against the RMSD of Cα atoms of equivalent residues in all pairs of TPI models. The data for three different sets of models are presented in green (SwissModel), blue (Modeller "Turbo") and red (Modeller "Automodel"), see Methods for details. The charged side chain atoms selected for RMSD calculations are Cζ, Nζ, Cγ and Cδ of the residues ARG, LYS, ASP and GLU, respectively. This plot shows clear differences between the three sets of models: the charged side chain atom RMSDs are on average 0.01, 0.1 and 1.0 Å for the SwissModel, ''Turbo'' and ''Automodel'' Modeller models, respectively, even though the Cα RMSDs differ insignificantly, being less than 1 Å in all three sets.
Gabdoulline et al. BMC Bioinformatics 2007 8:373 doi:10.1186/1471-2105-8-373