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})

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.