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>. | 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'' | 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> | |||
:<math>\operatorname{RMSD}= \sqrt{\frac{\sum_{i=1}^{N} (d_{i})^2}{N}}</math> | [[Image:Rmsd-equation.png]] | ||
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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. | ||
