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![[Figure 8]](ic5121fig8mag.jpg)
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Figure 8
Example of the ProDy Flexibility Hub workflow connected to Zernike3D to perform an advanced analysis of the motions of the SARS-CoV-2 spike in the 3Down conformation. (a) shows the main pipeline followed to execute the ProDy analysis. The connection to the Zernike3D results described in Fig. 6 ![[link]](../../../../../../logos/arrows/d_arr.gif){kind=small} is performed using structural models in PCA and NMA. These structures as well as the canonical closed and locked structures (PDB entries 6vxx and 6xr8) are aligned into an ensemble that is then used for PCA, revealing motions such as that shown in (b). The conformational landscape can be visualized by a projection of the ensemble of aligned structures onto the first three principal components (PCs) as shown in (c). (b) shows an example of the motions along PC2, which contributes most of the variation (after PC1 that distinguishes the locked and unlocked conformations), using structures generated by adding the PC2 vector to the average structure using a vector size equivalent to an r.m.s.d. of 4 Å. (c) shows the ProDy PCA projection representation of the conformational landscape for the 3Down conformations selected from the Zernike3D landscape and the locked and closed conformations. It should be noted that the projections are presented on the scale of r.m.s.d.s, demonstrating a very small conformational variability of <1 Å for PC2 and PC3. (d) shows a comparison of the PCA components with the NMA modes from the aligned reference structure as a directional overlap matrix of correlation cosines coloured from low correlations in blue to high correlations in red. |
![[Figure 8]](ic5121fig8.jpg)
 | STRUCTURAL BIOLOGY |
ISSN: 2059-7983
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