Normal mode analysis TSD

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Revision as of 19:51, 26 July 2012 by Reeb (talk | contribs)

The journal for this task can be found here.

WEBnm

ElNemo

wip


    What information do the different servers provide?
   How are the normal modes calculated, that is from which part of the structure? How many normal modes could in principle be calculated for your protein without any cutoff.
   Visualize the modes (provided by server or using for example PyMol or VMD) and describe what movements you observe: hinge-movement, “breathing”…
   Which regions of your protein are most flexible, most stable?
   Can you identify domains for your protein? Compare to the CATH, SCOP and Pfam domains of your protein.
   Can you observe notable differences between the normal modes calculated by the different servers?
   For WEBnm@ try the amplitude scaling and vectors option.
   Try the comparison/upload of second structure option, if: (i) you have PDB structures in different conformations or (ii) your protein has a bound ligand. Then either upload a structure with and one without the ligand, or delete the ligand in your structure. Note: Due to the force field that considers only C_alpha atoms, only changes in the backbone will give results. The model does not resolve changes in side-chain positions or SNPs.


Comparison to Molecular Dynamics

   When your MD simulations are finished, compare the lowest-frequency normal modes with your MD simulation using visualization software, e.g. PyMol or VMD. Can you observe different movements or similar dynamics? If possible, compare an overlay of the lowest-frequency modes to your MD simulation. You can superimpose the normal modes for example in VMD.
   What are the advantages and disadvantages of NMA compared to MD?