RMSD between structures - Revision history

Eric Martz at 18:03, 27 October 2024

2024-10-27T18:03:36Z

← Older revision		Revision as of 18:03, 27 October 2024
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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>.		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>.

	For N deviations ''d'',<br>		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:
	~~[[Image:Rmsd-equation.png]]<!--~~ since <math> is not implemented in Proteopedia, I generated this 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>
	:<math>\operatorname{RMSD}= \sqrt{\frac{\sum_{i=1}^{N} (d_{i})^2}{N}}</math>		[[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.		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.

Eric Martz at 18:00, 27 October 2024

2024-10-27T18:00:48Z

← Older revision		Revision as of 18:00, 27 October 2024
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	For N deviations ''d'',<br>		For N deviations ''d'',<br>
	[[Image:Rmsd-equation.png]]		[[Image:Rmsd-equation.png]]<!-- since <math> is not implemented in Proteopedia, I generated this in Wikipedia on a scratch page, and then took a snapshot. Code in wikipedia:
			:<math>\operatorname{RMSD}= \sqrt{\frac{\sum_{i=1}^{N} (d_{i})^2}{N}}</math>
			-->

	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.		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.

Eric Martz at 17:57, 27 October 2024

2024-10-27T17:57:41Z

← Older revision		Revision as of 17:57, 27 October 2024
Line 1:		Line 1:
	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>.		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'',<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==		==See Also==

Eric Martz at 18:59, 23 October 2024

2024-10-23T18:59:17Z

← Older revision		Revision as of 18:59, 23 October 2024
Line 1:		Line 1:
	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>.		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.		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.

	==See Also==		==See Also==

Eric Martz: New page: 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 shou...

2024-10-23T18:54:03Z

New page: 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 shou...

New page

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.

==See Also==
*[[Structure superposition tools]]
*[[Calculating GDT TS]], the comparison used in the [[CASP]] competitions.

==References==
<references />