Difference between revisions of "Normal mode analysis (Phenylketonuria)"
From Bioinformatikpedia
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elNémo computes models for the given protein 1J8U. Following informations are provided for those modes: <br> |
elNémo computes models for the given protein 1J8U. Following informations are provided for those modes: <br> |
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*PDB-files with the conformations of the modes |
*PDB-files with the conformations of the modes |
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| − | *animations of the modes |
+ | *animations of the modes of three different sites |
*CA-vari (calculates distance fluctuations between all C-alpha atoms) |
*CA-vari (calculates distance fluctuations between all C-alpha atoms) |
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*R<sup>2</sup> (visualization of the mean square displacement of all C-alpha atoms associated with a given mode) |
*R<sup>2</sup> (visualization of the mean square displacement of all C-alpha atoms associated with a given mode) |
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Revision as of 11:33, 28 July 2013
Page still under construction!!!
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. Following informations are provided for those modes:
- 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 (visualization of the mean square displacement of all C-alpha atoms associated with a given mode)
- 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: 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/>
