# DBT JRF 2020 — Question 118

Exam: DBT JRF 2020 · Section: B · Topic: Bioinformatics · Difficulty: Medium

## Question

Which of the following represents a quantitative measure of the structural similarity between two proteins?

## Options

- **A.** root mean square deviation
- **B.** root mean square distance
- **C.** revised mode square deviation
- **D.** standard deviation

## Answer

Option A

## Explanation

Root Mean Square Deviation (RMSD) is the standard quantitative measure of structural similarity between two protein structures: $\text{RMSD} = \sqrt{\dfrac{1}{N}\sum_{i=1}^{N} d_i^2}$ , where $d_i$ is the distance between the $i$ th pair of equivalent atoms (typically C $\alpha$ atoms) 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.

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