Difference between revisions of "Normal Mode Analysis of ARSA"
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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. <br> |
In this TASK, we apply different NMA methods to our protein ARSA to investigate the flexibility and motions of the structure. <br> |
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− | For most methods, we were able generate animated pictures to visualise the results. We used |
+ | 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: |
<code> |
<code> |
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gifsicle --delay=5 --loop --colors 256 *.gif > anim.gif |
gifsicle --delay=5 --loop --colors 256 *.gif > anim.gif |
Revision as of 10:15, 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 |
mode 7 | ![]() |
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mode 8 | ![]() |
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mode 9 | ![]() |
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mode 10 | ![]() |
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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 |
Mode 7 | ![]() |
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Mode 8 | ![]() |
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Mode 9 | ![]() |
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Mode 10 | ![]() |
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Mode 11 | ![]() |
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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 | |
Motion | ![]() |
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Distance | ![]() |
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Fluctuations | ![]() |
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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 | |
Motion | ![]() |
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Fluctuations | ![]() |
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NOMAD-Ref
NMA of ARSA
mode 7 | mode 8 | mode 9 | mode 10 | mode 11 | |
Motion | ![]() |
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Distance | ![]() |
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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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