Question: what is the threshold RMSD value for determining protein structure similarity
gravatar for smjsardar
23 months ago by
smjsardar0 wrote:

I predicted mutated protein structure (via MODELLER) from a reference protein structure. I then compared these mutant structures with my reference by superimposing and finding the RMSD values. Now what value of RMSD would determine if my mutated protein structures are different from my reference? Can I say values above 0.5 Angstrom means there is a significant difference between the two structures?

rmsd protein structure • 2.7k views
ADD COMMENTlink modified 17 months ago by jgreener260 • written 23 months ago by smjsardar0
gravatar for Joe
23 months ago by
United Kingdom
Joe18k wrote:

There's no magic number. An RMSD of less than about 2 Å would generally be considered very close, but there's no absolute rule. A single mutation could have a very profound effect on structure, or could make essentially no difference depending on where it is in the structure.

You need to think about your actual biological question.

ADD COMMENTlink modified 23 months ago • written 23 months ago by Joe18k
gravatar for jgreener
17 months ago by
United Kingdom
jgreener260 wrote:

To add to the above answer, RMSD is dependent on the size of the protein.

If you are looking for a cut-off score, with all the caveats that entails, I would recommend using TM-score (or the related TM-align). TM-score runs from 0 to 1 and a TM-score of 0.5 or higher indicates that the two structures probably have the same fold.

Check out the CASP website and papers for more on this, they think pretty hard about this problem.

ADD COMMENTlink written 17 months ago by jgreener260
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