RMSD between structures: Difference between revisions

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The root mean square deviation (RMSD) "is a measure of the average deviation in distance between aligned Cα atoms in 3D superimposition. For sequences sharing 50% identity, this should be around 1.0 [Å]."<ref name="holm-using">PMID:32006276</ref>.

~~Similarly~~, ~~the~~ RMSD between two independently-determined [[X-ray crystallography]] structures of the same protein is typically about 1.0 Å. Larger values of the RMSD indicate less similarity between the two structures. RMSD is useful for structures with substantial similarity, but less useful when the structures diverge more. [[Calculating GDT TS|GDT TS]] has been used in the [[CASP]] competitions to detect more remote similarities.

For N deviations ''d'' <ref name="equation">since <math> is not implemented in Proteopedia, I generated this equation in Wikipedia on a scratch page, and then took a snapshot. Code in wikipedia:

<nowiki>:<math>\operatorname{RMSD}= \sqrt{\frac{\sum_{i=1}^{N} (d_{i})^2}{N}}</math></nowiki></ref>,<br>

[[Image:Rmsd-equation.png]]

The RMSD between two independently-determined [[X-ray crystallography]] structures of the same protein is typically about 1.0 Å. Larger values of the RMSD indicate less similarity between the two structures.

RMSD is useful for structures with substantial similarity, but less useful when the structures diverge more. [[Calculating GDT TS|GDT TS]] has been used in the [[CASP]] competitions to detect more remote similarities.

==See Also==

RMSD between structures: Difference between revisions

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 The root mean square deviation (RMSD) "is a measure of the average deviation in distance between aligned C&alpha; atoms in 3D superimposition. For sequences sharing 50% identity, this should be around 1.0 [&Aring;]."<ref name="holm-using">PMID:32006276</ref>.
-Similarly, the RMSD between two independently-determined [[X-ray crystallography]] structures of the same protein is typically about 1.0 &Aring;. Larger values of the RMSD indicate less similarity between the two structures. RMSD is useful for structures with substantial similarity, but less useful when the structures diverge more. [[Calculating GDT TS|GDT TS]] has been used in the [[CASP]] competitions to detect more remote similarities.
+For N deviations ''d'' <ref name="equation">since &lt;math&gt; is not implemented in Proteopedia, I generated this equation in Wikipedia on a scratch page, and then took a snapshot. Code in wikipedia:
+<nowiki>:<math>\operatorname{RMSD}= \sqrt{\frac{\sum_{i=1}^{N} (d_{i})^2}{N}}</math></nowiki></ref>,<br>
+[[Image:Rmsd-equation.png]]
+The RMSD between two independently-determined [[X-ray crystallography]] structures of the same protein is typically about 1.0 &Aring;. Larger values of the RMSD indicate less similarity between the two structures.
+RMSD is useful for structures with substantial similarity, but less useful when the structures diverge more. [[Calculating GDT TS|GDT TS]] has been used in the [[CASP]] competitions to detect more remote similarities.
 ==See Also==