RMSD of a structural superposition

Question

[silvia.caprari84]

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.

Answer 1

[evo_genomics]

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

[v27]

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