# DBT JRF 2022 — Question 132

Exam: DBT JRF 2022 · Section: B · Topic: Bioinformatics › Structural Bioinformatics - RMSD · Difficulty: Medium

## Question

The measure of similarity between two structurally aligned macromolecules is:

## Options

- **A.** Median Distance between the Centroids (MDC)
- **B.** Root Mean Square Deviation (RMSD)
- **C.** Squared Mean Distance between atoms (SMD)
- **D.** Mean Distance between Centroids (DBC)

## Answer

Option B

## Explanation

RMSD — measure of structural similarity: RMSD (Root Mean Square Deviation) is the standard metric for comparing the structural similarity of two macromolecules after optimal superimposition: $\text{RMSD} = \sqrt{\frac{1}{N} \sum_{i=1}^{N} |\mathbf{r}_i^A - \mathbf{r}_i^B|^2}$ where $\mathbf{r}_i^A$ and $\mathbf{r}_i^B$ are the positions of corresponding atoms (typically C $\alpha$ carbons) in structures A and B. Interpretation: • RMSD < 1 Å: Very similar structures (essentially the same fold) • RMSD 1–3 Å: Similar fold, local differences • RMSD > 3 Å: Different folds Applications: • Comparing experimental vs. predicted structures • Molecular dynamics simulation analysis (structural drift) • Protein structure alignment (DALI, TM-score also used) Answer: RMSD calculates the average distance between corresponding atoms of two superimposed structures; lower RMSD = more similar.

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