Evaluation of the structural quality of modeled proteins by using globularity criteria

BMC Structural Biology

Table 2 Correlation coefficients in the four structural classes.

	mainly-alpha	mainly-beta	alpha/beta	alpha+beta
H-bonds
MM-type	0.95	0.83	0.97	0.96
MS-type	0.61	0.49	0.83	0.79
SM-type	0.70	0.39	0.85	0.81
SS-type	0.67	0.41	0.82	0.81
Total	0.93	0.80	0.97	0.95
Total Accessibility
polar-	0.89	0.89	0.93	0.94
non polar-	0.92	0.90	0.95	0.92
Total	0.95	0.93	0.96	0.94
Void
total void volumes	0.87	0.9	0.92	0.91
void numbers	0.97	0.91	0.99	0.97
water
molecule number	0.93	0.91	0.97	0.93
protein-water H-bonds	0.8	0.76	0.71	0.73
protein-water H-bonds/total accessibility	0.84	0.81	0.78	0.73

The correlation coefficients are evaluated between the molecular weights and the different types of H-bonds, the total solvent accessibility and its components, the number of water molecules and the related H-bonds between residue proteins and water molecules, and void number and total void volumes (calculated with probe = 0) obtained for each protein belonging to "mainly-alpha, "mainly-beta", "alpha/beta" and "alpha+beta" classes. The last row reports the correlation coefficient between the total accessibility and the number of H-bonds between residue proteins and water molecules.

ISSN: 1472-6807