Difference between revisions of "Normal Mode Analysis of Glucocerebrosidase"

From Bioinformatikpedia
(→‎WEBnm@)
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=== WEBnm@ ===
  
=== WEBnm@ ===
   
−
WEBnm@ is a web-server which provides automated computation and analysis of low-frequency normal modes of proteins. <ref>Hollup SM, Sælensminde G, Reuter N. WEBnm@: a web application for normal mode analysis of proteins BMC Bioinformatics. 2005 Mar 11;6(1):52 </ref>
 +
WEBnm@ is a web-server which provides automated computation and analysis of low-frequency normal modes of proteins. For an input structure file in PDB format, the normal modes are calculated and a series of automated calculations (normalized squared atomic displacements, vector field representation and an animation of the first six vibrational modes). Additional to the single analysis (calculating lowest frequency normal modes for one protein), the server offers a comperative analysis. In this analysis, the normal modes of a set of aligned sequences are calculated and compared. This feature is still under development. <ref>Hollup SM, Sælensminde G, Reuter N. WEBnm@: a web application for normal mode analysis of proteins BMC Bioinformatics. 2005 Mar 11;6(1):52 </ref>
   
  +
''' Usage '''
  +
* Webserver: http://apps.cbu.uib.no/webnma/home
  +
* Input:
  +
** Single Analysis: structure file in PDB format
  +
** Comparative Analysis: structure files in PDB format and sequence files in fasta format
  +
<br/>
 
''' Results '''
  
''' Results '''
   
  +
Figure 1 to 5 show the first five vibrational modes (modes 7 to 11) calculated with WEBnm@ for the structure of glucocerebrosidase (2NTO). Modes 1-6 are rigid body motions without frequency.
   
 
[[File:Webnma_nm7_glucocerebrosidase.gif |thumb|center|500px|'''Figure 1:''' Normal Mode 7 calculated with WEBnm@]]
  
[[File:Webnma_nm7_glucocerebrosidase.gif |thumb|center|500px|'''Figure 1:''' Normal Mode 7 calculated with WEBnm@]]
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[[File:Webnma_nm11_glucocerebrosidase.gif |thumb|center|500px|'''Figure 5:''' Normal Mode 11 calculated with WEBnm@]]
  
[[File:Webnma_nm11_glucocerebrosidase.gif |thumb|center|500px|'''Figure 5:''' Normal Mode 11 calculated with WEBnm@]]
   
  +
''' Discussion '''
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=== ''elNémo'' ===
  
  +
  +
=== ''ElNémo'' ===
  +
  +
''ElNémo'' is a web-server based on the Elastic Network Model. The tool computes, visualizes and analyses low-frequency normal modes of large macro-molecules. Any size of proteins can be treated as ''ElNémo'' uses a 'rotation-translation-block' approximation. <ref>K. Suhre & Y.H. Sanejouand, ElNemo: a normal mode web-server for protein movement analysis and the generation of templates for molecular replacement. Nucleic Acids Research, 32, W610-W614, 2004. </ref>
  +
  +
''' Usage'''
  +
*Webserver: http://www.igs.cnrs-mrs.fr/elnemo/start.html
  +
* Input:
  +
*** structure file in PDB format
  +
*** supplementary options for NMA calculation (number of normal modes to be calculated, minimum and maximum perturbation and stepsize between DQMIN and DQMAX)
  +
*** options for computing the eigenmodes (NRBL and cutoff to identify elastic interactions)
   
 
''' Results '''
  
''' Results '''
   
   
−
[[File:Elnemo_nm7_glucocerebrosidase.gif |thumb|center|500px|'''Figure 6:''' Normal Mode 7 calculated with ''elNémo'']]
 +
[[File:Elnemo_nm7_glucocerebrosidase.gif |thumb|center|500px|'''Figure 6:''' Normal Mode 7 calculated with ''ElNémo'']]
−
[[File:Elnemo_nm8_glucocerebrosidase.gif |thumb|center|500px|'''Figure 7:''' Normal Mode 8 calculated with ''elNémo'']]
 +
[[File:Elnemo_nm8_glucocerebrosidase.gif |thumb|center|500px|'''Figure 7:''' Normal Mode 8 calculated with ''ElNémo'']]
−
[[File:Elnemo_nm9_glucocerebrosidase.gif |thumb|center|500px|'''Figure 8:''' Normal Mode 9 calculated with ''elNémo'']]
 +
[[File:Elnemo_nm9_glucocerebrosidase.gif |thumb|center|500px|'''Figure 8:''' Normal Mode 9 calculated with ''ElNémo'']]
−
[[File:Elnemo_nm10_glucocerebrosidase.gif |thumb|center|500px|'''Figure 9:''' Normal Mode 10 calculated with ''elNémo'']]
 +
[[File:Elnemo_nm10_glucocerebrosidase.gif |thumb|center|500px|'''Figure 9:''' Normal Mode 10 calculated with ''ElNémo'']]
−
[[File:Elnemo_nm11_glucocerebrosidase.gif |thumb|center|500px|'''Figure 10:''' Normal Mode 11 calculated with ''elNémo'']]
 +
[[File:Elnemo_nm11_glucocerebrosidase.gif |thumb|center|500px|'''Figure 10:''' Normal Mode 11 calculated with ''ElNémo'']]
   
 
''' Discussion '''
  
''' Discussion '''
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== Comparison NMA / MD ==
  
== Comparison NMA / MD ==
  +
  +
== References ==
  +
<references/>

Revision as of 23:54, 15 July 2011

Introduction

Elastic and Gaussian Network Models

WEBnm@

WEBnm@ is a web-server which provides automated computation and analysis of low-frequency normal modes of proteins. For an input structure file in PDB format, the normal modes are calculated and a series of automated calculations (normalized squared atomic displacements, vector field representation and an animation of the first six vibrational modes). Additional to the single analysis (calculating lowest frequency normal modes for one protein), the server offers a comperative analysis. In this analysis, the normal modes of a set of aligned sequences are calculated and compared. This feature is still under development. <ref>Hollup SM, Sælensminde G, Reuter N. WEBnm@: a web application for normal mode analysis of proteins BMC Bioinformatics. 2005 Mar 11;6(1):52 </ref>

Usage

  • Webserver: http://apps.cbu.uib.no/webnma/home
  • Input:
    • Single Analysis: structure file in PDB format
    • Comparative Analysis: structure files in PDB format and sequence files in fasta format


Results

Figure 1 to 5 show the first five vibrational modes (modes 7 to 11) calculated with WEBnm@ for the structure of glucocerebrosidase (2NTO). Modes 1-6 are rigid body motions without frequency.

Figure 1: Normal Mode 7 calculated with WEBnm@
Figure 2: Normal Mode 8 calculated with WEBnm@
Figure 3: Normal Mode 9 calculated with WEBnm@
Figure 4: Normal Mode 10 calculated with WEBnm@
Figure 5: Normal Mode 11 calculated with WEBnm@

Discussion

ElNémo

ElNémo is a web-server based on the Elastic Network Model. The tool computes, visualizes and analyses low-frequency normal modes of large macro-molecules. Any size of proteins can be treated as ElNémo uses a 'rotation-translation-block' approximation. <ref>K. Suhre & Y.H. Sanejouand, ElNemo: a normal mode web-server for protein movement analysis and the generation of templates for molecular replacement. Nucleic Acids Research, 32, W610-W614, 2004. </ref>

Usage

  • Webserver: http://www.igs.cnrs-mrs.fr/elnemo/start.html
  • Input:
      • structure file in PDB format
      • supplementary options for NMA calculation (number of normal modes to be calculated, minimum and maximum perturbation and stepsize between DQMIN and DQMAX)
      • options for computing the eigenmodes (NRBL and cutoff to identify elastic interactions)

Results


Figure 6: Normal Mode 7 calculated with ElNémo
Figure 7: Normal Mode 8 calculated with ElNémo
Figure 8: Normal Mode 9 calculated with ElNémo
Figure 9: Normal Mode 10 calculated with ElNémo
Figure 10: Normal Mode 11 calculated with ElNémo

Discussion

Anisotropic Network Model

oGNM

NOMAD-Ref

Discussion

All-atom NMA

Comparison NMA / MD

References

<references/>

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