Question: what is the threshold RMSD value for determining protein structure similarity
0
gravatar for smjsardar
7 months ago by
smjsardar0
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 • 810 views
ADD COMMENTlink modified 8 weeks ago by jgreener100 • written 7 months ago by smjsardar0
2
gravatar for jrj.healey
7 months ago by
jrj.healey13k
United Kingdom
jrj.healey13k 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 7 months ago • written 7 months ago by jrj.healey13k
1
gravatar for jgreener
8 weeks ago by
jgreener100
United Kingdom
jgreener100 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 8 weeks ago by jgreener100
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