A restraint molecular dynamics and simulated annealing approach for protein homology modeling utilizing mean angles

Table 7 Comparison between model structures and experimental structures for HPr

Structures	Quantities^a	NMR target structure	X-ray target structure
X-ray structure	backbone RMSD [nm]	0.106	0
	heavy atom RMSD [nm]	0.273	0
	R-factor	0.073	0
best NMR structure	backbone RMSD [nm]	0	0.106
	heavy atom RMSD [nm]	0	0.273
	R-factor	0	0.072
best model structure	backbone RMSD [nm]	0.169	0.147
	heavy atom RMSD [nm]	0.273	0.253
	R-factor	0.093	0.076
model structure bundle	backbone RMSD [nm]	0.178	0.154
	heavy atom RMSD [nm]	0.277	0.258
	R-factor	0.097	0.081

^aBackbone RMSDs include N^H, C^α, and C' atoms. Heavy atoms include all atoms except protons. RMSDs are pairwise RMSDs. R-factors are calculated using the R-factor R₃ according to [46] including only signals arising from backbone protons.

ISSN: 1471-2105