[MMTK] Deformation analysis

James Starlight jmsstarlight at gmail.com
Fri Nov 4 10:48:27 UTC 2011

Dear Konrad,

I want to perform deformation analysis in the MMTK ( something like this
I've found in your paper where It could be done via NM@ server )

I have 2 x-ray structures of the GPCR receptor ( active and innactive form)

Firtly, I want to compure RMSD  and obain deformation vector wich would
describe the change between two structures of my protein.

Then I'd like to make comparison of that deformation vector with the soft
modes calculated in NMA and ENM for the innactive structure.

So I have some questions:

1) The molecule of the receptor cionsist of 7 alpha-helices domens
Could the NMA in general be suitable for investigation of the activation of
the receptors ? In this case activation process is linked with the
displacement of the some alpha-helices of the receptor. But as I've
inderstood NMA is more suitable for the investigation of the displacement
of the whole domains consisted of the specific monomer for instance.

2) As I understood the ENM doest require for the minimisation of my initial
structure. But after some of my analysis some of the obtained modes were
negative wich could indicate in case of NMA that my structure could not be
minimised properly. Why negative modes might occur in case of ENM?

3) Where I can obtain information about such deformation analysis if it
possible via MMTK ? I found that  MMTK.Deformation module could be
something that I need :) But Its not quite understood for me how to build
deformation vector beetwen my structures.

4) Finally I want to compare def. vctor with the soft modes as well with
the ensemble modes. So in first place I need in the directly comparison of
the fluctuations along each  deformation direction. And in the second place
I need in something like cumulative overlap beetwen def vector and the soft
modes enssemble.  Would  this strategy  be correct?

Thanks for help again,

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