Task 10 (MSUD)

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Revision as of 17:16, 24 July 2013 by Schillerl (talk | contribs) (WEBnm@)


Lab journal


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.

Vector representations of modes 7 and 9:

<gallery widths=500px heights=250px perrow=2"> File:MSUD_mode7.png| Normal mode 7 of 2BFF, alpha and beta chain move against each other. File:MSUD_mode9.png| Normal mode 9 of 2BFF, end of alpha chain moves strongly. </gallery