Difference between revisions of "Normal Mode Analysis of ARSA"
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== Introduction == |
== Introduction == |
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Normal Mode Analysis (NMA) is a very useful tool to analyse large-scale motions in proteins. There are two approaches. In the first approach, all-atoms were used to calculate the harmonic motions. As this procedure needs a lot of memory, the elastic network model was developed, which does not take all interactions into account. Like this the memory needed can be dramatically reduced and the method can be applied to larger proteins. <br> |
Normal Mode Analysis (NMA) is a very useful tool to analyse large-scale motions in proteins. There are two approaches. In the first approach, all-atoms were used to calculate the harmonic motions. As this procedure needs a lot of memory, the elastic network model was developed, which does not take all interactions into account. Like this the memory needed can be dramatically reduced and the method can be applied to larger proteins. <br> |
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| − | In this TASK, we apply different NMA methods to our protein ARSA to investigate the flexibility and motions of the structure. |
+ | In this TASK, we apply different NMA methods to our protein ARSA to investigate the flexibility and motions of the structure. <br> |
| + | For most methods, we were able generate animated pictures to visualise the results. We used [[http://www.lcdf.org/gifsicle/ || gifsicle]] to generate the animated gifs: |
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| + | <code> |
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| + | gifsicle --delay=5 --loop --colors 256 *.gif > anim.gif |
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| + | </code> |
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== WEBnm@ == |
== WEBnm@ == |
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Revision as of 09:14, 12 August 2011
Contents
Introduction
Normal Mode Analysis (NMA) is a very useful tool to analyse large-scale motions in proteins. There are two approaches. In the first approach, all-atoms were used to calculate the harmonic motions. As this procedure needs a lot of memory, the elastic network model was developed, which does not take all interactions into account. Like this the memory needed can be dramatically reduced and the method can be applied to larger proteins.
In this TASK, we apply different NMA methods to our protein ARSA to investigate the flexibility and motions of the structure.
For most methods, we were able generate animated pictures to visualise the results. We used [|| gifsicle] to generate the animated gifs:
gifsicle --delay=5 --loop --colors 256 *.gif > anim.gif
WEBnm@
We used | http://www.lcdf.org/gifsicle/ to generate the animated gifs:
gifsicle --delay=5 --loop --colors 256 *.gif > anim.gif
| Mode | Motion | Vecors | Displacement |
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| mode 11 | 
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| mode 12 | 
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ElNemo
| Mode | Pymol animation | picture 1 from ElNemo | picture 2 from ElNemo | picture 3 from ElNemo | Fluctuations |
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Anisotropic Network Model web server
for file in *.png; do convert "$file" "$(basename $file .png).gif";done
| mode 1 | mode 2 | mode 3 | mode 4 | mode 5 | |
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oGNM – Gaussian network model
http://ignm.ccbb.pitt.edu/ognm/1960654514/temp/index.htm
| mode 7 | mode 8 | mode 9 | mode 10 | mode 11 | |
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NOMAD-Ref
NMA of ARSA
| mode 7 | mode 8 | mode 9 | mode 10 | mode 11 | |
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NMA of 1BPT
| Temperature | mode | mode 8 | mode 9 | mode 10 | mode 11 |
| 600K (all-atom) | 
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| 2000K (all-atom) | 
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| Elastic Network | 
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