Question: RMSD of a structural superposition
1
gravatar for silvia.caprari84
5.8 years ago by
Germany
silvia.caprari8450 wrote:

Hi,

I am doing some structural comparisons with the visualization program Chimera to see similarities within a dataset of proteins. I was wondering how I evaluate if a superposition is significant or not. I know that the RSMD is typically used,but which value of RMSD (threshold) is it better to choose in order to discern between significant and no significant superpositions?

Furthermore, I think that I have to consider even the number of atoms aligned..otherwise I could even  have a good RMSD value , but maybe the number of atoms superposed is too low compared to the length of the two proteins, right?. So, how can I report the data concerning the superpositions and be able to say that some superpositions are significant and other are not? Is there a value/parameter/calculation allowing to consider RMSD and number residues aligned on total length of the protein together?

Any suggestion would be really appreciated.

Thank you very much in advance

Silvia.

rmsd • 3.2k views
ADD COMMENTlink modified 5.7 years ago by evo_genomics60 • written 5.8 years ago by silvia.caprari8450
0
gravatar for evo_genomics
5.7 years ago by
evo_genomics60
Pakistan
evo_genomics60 wrote:

RMSD value should be close to zero. Higher the RMSD value, more target structure deviate from template structure. RMSD value of full length structure should be considered

 

ADD COMMENTlink written 5.7 years ago by evo_genomics60

could you give reference to an article that supports RMSD value should be close to zero

ADD REPLYlink written 2.6 years ago by v2710
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