Difference between revisions of "Task 10 (MSUD)"
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The server gives eigenvalues for modes 7-56, deformation energies for modes 7-20 and atomic displacement and visualization for modes 7-12. |
The server gives eigenvalues for modes 7-56, deformation energies for modes 7-20 and atomic displacement and visualization for modes 7-12. |
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| + | In all modes that are visualized by the server, a movement of alpha and beta chain against each other can be observed, sometimes there is a hinge-movement (mode 7) and in other modes there is a torsion between the subunits. In most modes, a part at the end of alpha subunit (BCKDHA), consisting of 3 small helices that reach into the beta subunit, moves independently from the rest of the alpha subunit but together with beta subunit. An exception is mode 9, where this part moves a lot compared to the rest of the protein. Vector representations of modes 7 and 9: |
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| − | Vector representations of modes 7 and 9: |
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<gallery widths=500px heights=250px perrow=2"> |
<gallery widths=500px heights=250px perrow=2"> |
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Revision as of 16:25, 24 July 2013
Contents
Results
WEBnm@
The informations that are provided on the results page include:
- deformation energies and eigenvalues for the lowest-frequency non-trivial modes
- atomic displacement and fluctuation plots
- mode visualization with Jmol and vector field represention of modes
- correlation matrix for motions between Calphas
- overlap analysis for different conformations of the same protein
For the calculation of normal modes, WEBnm@ takes only Calpha atoms. The mass of the whole residue is assigned to its Calpha atom for the analysis.
The server gives eigenvalues for modes 7-56, deformation energies for modes 7-20 and atomic displacement and visualization for modes 7-12.
In all modes that are visualized by the server, a movement of alpha and beta chain against each other can be observed, sometimes there is a hinge-movement (mode 7) and in other modes there is a torsion between the subunits. In most modes, a part at the end of alpha subunit (BCKDHA), consisting of 3 small helices that reach into the beta subunit, moves independently from the rest of the alpha subunit but together with beta subunit. An exception is mode 9, where this part moves a lot compared to the rest of the protein. Vector representations of modes 7 and 9:
Normal mode 7 of 2BFF, alpha and beta chain move against each other.
Normal mode 9 of 2BFF, end of alpha chain moves strongly.
