Difference between revisions of "Normal mode analysis (Phenylketonuria)"
From Bioinformatikpedia
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=== elNémo === |
=== elNémo === |
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| + | elNémo computes models for the given protein 1J8U. The analyses of the five modes with lowest normal modes are shown below. Following informations are provided for those modes: <br> |
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| − | elNémo provides following outcomes: <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 |
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*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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| + | *Frequency and collectivity of the modes |
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*B-factor analysis: Correlation= 0.534 for 307 C-alpha atoms |
*B-factor analysis: Correlation= 0.534 for 307 C-alpha atoms |
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*RMSD: only if two structures are used |
*RMSD: only if two structures are used |
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Revision as of 11:18, 28 July 2013
Page still under construction!!!
Contents
Summary
...
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
...
Mode 8
...
Mode 9
...
Mode 10
...
Mode 11
...
Mode 12
...
elNémo
elNémo computes models for the given protein 1J8U. The analyses of the five modes with lowest normal modes are shown below. Following informations are provided for those modes:
- PDB-files with the conformations of the modes
- animations of the modes
- 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
- B-factor analysis: Correlation= 0.534 for 307 C-alpha atoms
- RMSD: only if two structures are used
Mode 7
...
Mode 8
...
Mode 9
...
Mode 10
...
Mode 11
...
VMD
...
References
<references/>
