Which of the following represents a quantitative measure of the structural similarity between two proteins?
Which of the following represents a quantitative measure of the structural similarity between two proteins?
Select an option to attempt
Correct Answer: Option A
Explanation
Root Mean Square Deviation (RMSD) is the standard quantitative measure of structural similarity between two protein structures:, whereis the distance between theth pair of equivalent atoms (typically Catoms) in the two structures after optimal superimposition. Lower RMSD = more similar structures. Thresholds: RMSD <1 Å → essentially identical; RMSD 1–2 Å → closely related; RMSD >3 Å → substantially different. Used in: model quality assessment (comparison of predicted vs experimental structure — AlphaFold2 achieves median RMSD <1 Å on CASP14 targets); structural alignment (Dali, CE, TM-align); molecular dynamics trajectory analysis. TM-score and GDT-TS are additional structural similarity metrics that are less sensitive to local outliers.