Question

The root mean square deviation (RMSD), without the size dependency correction is?

(a) \(\sum_{i=1}^N \frac{D_i^2}{N}\)

(b) \(\sum_{i=1}^N \frac{D_i^2}{N + 1}\)

(c) \(\sum_{i=1}^N \frac{D_i^2}{N x N}\)

(d) \(\sum_{i=1}^N \frac{D_i^2}{N – 1}\)

The question was posed to me in an internship interview.

My question comes from Protein Structure Comparison in chapter Structural Bioinformatics of Bioinformatics

Answer 1

Correct answer is (a) \(\sum_{i=1}^N \frac{D_i^2}{N}\)

For explanation: An important measurement of the structure fit during superposition is the distance between equivalent positions on the protein structures. This requires using a least square-fitting function called root mean square deviation (RMSD), which is the square root of the averaged sum of the squared differences of the atomic distances. Here D is the distance between coordinate data points and N is the total number of corresponding residue pairs.