Difference between revisions of "Gaucher Task09 Protocol"

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== WEBnm@ ==
 
== WEBnm@ ==
   
  +
The online server of [http://apps.cbu.uib.no/webnma/home WEBnm@] was used.
  +
  +
Single PDB Analysis: input PDB structure file and select which chain will be treated. In our case, we selected chain A
  +
  +
Comparative Analysis: input PDB structure files and FASTA sequence file
   
 
== ElNemo ==
 
== ElNemo ==
  +
  +
The online server of [http://www.igs.cnrs-mrs.fr/elnemo/start.html ElNemo] was used.
  +
  +
Input the PDB structure file. There are Supplementary options for the calculation of NMA perturbed models including:
  +
*number of normal modes to be calculated,
  +
*minimum perturbation
  +
*maximum perturbation
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*stepsize between DQMIN and DQMAX)
  +
  +
And there are expert options for computing the eigenmodes.
  +
*NRBL
  +
*CUTOFF
  +
  +
One can also compare two different conformations for a protein structure by uploading the second PDB structure file.

Latest revision as of 14:07, 16 July 2012

WEBnm@

The online server of WEBnm@ was used.

Single PDB Analysis: input PDB structure file and select which chain will be treated. In our case, we selected chain A

Comparative Analysis: input PDB structure files and FASTA sequence file

ElNemo

The online server of ElNemo was used.

Input the PDB structure file. There are Supplementary options for the calculation of NMA perturbed models including:

  • number of normal modes to be calculated,
  • minimum perturbation
  • maximum perturbation
  • stepsize between DQMIN and DQMAX)

And there are expert options for computing the eigenmodes.

  • NRBL
  • CUTOFF

One can also compare two different conformations for a protein structure by uploading the second PDB structure file.