Angstroms And Rmsd

Question

[Harpalss]

I've noticed on a few protein Modelling sites they state the following example by their models "12.1±4.4Å (RMSD)"

What is the connection between the RMSD and Angstroms?

Answer 1

[João Rodrigues]

RMSD stands for root-mean-square deviation, and it is a measure to assess the structural similarity between two macromolecules. It is calculated based on the spatial distance between pairs of equivalent atoms of the two structures and these are usually best represented in Å than in any other unit (meter, milimeter, etc). Sometimes you can also see it in nm for very very large structures.

If you have something like 12.2Å +- 4.4 it means that there was somewhere an average calculated in a collection of structures and the average RMSD is 12.2Å while the standard deviation in the collection is 4.4. For example, if you are comparing structures to a reference.

Answer 2

[Damian Kao]

[?]root mean squared deviation in bioinformatics[?]

Answer 3

[Woa]

There are some modified alternatives to RMSD for the measure of structural similiraty, albeit being a bit uncommon. You can use them as well.

http://www.ncbi.nlm.nih.gov/pubmed/11420449

http://www.ncbi.nlm.nih.gov/pubmed/7479700