Normal mode analysis (Phenylketonuria)
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Contents
Summary
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Normal Mode Analysis
Lab journal
For the analysis, we used the pdb structure 1J8U from the task before (Task 9 - Structure-based mutation analysis).
WEBnm@
Mode 7
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Mode 8
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Mode 9
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Mode 10
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Mode 11
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Mode 12
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elNémo
ElNémo computes models for the given protein 1J8U. Thereby it calculates 100 lowest-frequency modes and provides a lot of information about the modes with different parameters and visualizations:
- PDB-files with the conformations of the modes
- animations of the modes of three different sites
- CA-vari (calculates distance fluctuations between all C-alpha atoms)
- R2 residue mean square displacement of all C-alpha atoms
- Frequency and collectivity of the modes
<figtable id="frecol">
| First five modes | |||
|---|---|---|---|
| Mode | Frequency | Collectivity | |
| mode 7 | 1.00 | 0.5475 | |
| mode 8 | 1.02 | 0.4062 | |
| mode 9 | 1.36 | 0.2941 | |
| mode 10 | 1.43 | 0.0948 | |
| mode 11 | 1.60 | 0.3466 | |
</figtable>
- B-factor analysis for the correlation between observed and normal-mode-derived atomi displacement parameters:
- Correlation = 0.534 for 307 C-alpha atoms
- RMSD: only if two structures are used
The analyses of the five modes with lowest normal modes are shown below.
Mode 7
Mode 8
Mode 9
Mode 10
Mode 11
VMD
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References
<references/>
