Research Article
Three-Dimensional Molecular Modeling of a Diverse Range of SC Clan Serine Proteases
Table 5
Structural validation of the modeled SC proteases from Arabidopsis thaliana and Plasmodium falciparum.
| | Structural model | All-atom clashscore
(No/1000 atoms) | Rotamer outliers
(%) | RMSD of bond length
(Å) | RMSD of bond angle
(degree) |
| | X-ray structure (1YR2) | 3.76 | 2.40 | 0.240 | 2.76 | Homology model of
A. thaliana protease | 5.37 | 2.14 | 0.270 | 3.70 | | X-ray structure (1U2E) | 23.50 | 9.62 | 0.013 | 2.27 | Threading model of
P. falciparum protease | 11.30 | 4.50 | 0.028 | 3.26 |
| | | Average Verify3D-1D score | Normalized 3D profile score
(log2(Verify3D/) | ProSA
-score | ERRAT quality factor (%) |
| | X-ray structure (1YR2) | 0.46 | −10.53 | −9.68 | 95.2 | Homology model of
A. thaliana protease | 0.34 | −9.66 | −7.55 | 88.9 | | X-ray structure (1U2E) | 0.42 | −10.86 | −9.88 | 93.7 | Threading model of
P. falciparum protease | 0.29 | −9.58 | −4.53 | 75.5 |
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