Question

The root mean square deviation (RMSD), with the size dependency correction is?

(a) \(\frac{RMSD}{-1.3 + 0.5 ln⁡(N+1)}\)

(b) \(\frac{RMSD}{-1.3 + 0.5 ln⁡(N x N)}\)

(c) \(\frac{RMSD}{-1.3 + 0.5 ln⁡(N-1)}\)

(d) \(\frac{RMSD}{-1.3 + 0.5 ln⁡(N)}\)

I have been asked this question in final exam.

This interesting question is from Protein Structure Comparison in division Structural Bioinformatics of Bioinformatics

Answer 1

The correct answer is (d) \(\frac{RMSD}{-1.3 + 0.5 ln⁡(N)}\)

For explanation: In practice, only the distances between Cα carbons of corresponding residues are measured. The goal of structural comparison is to achieve a minimum RMSD. However, the problem with RMSD is that it depends on the size of the proteins being compared. For the same degree of sequence identity, large proteins tend to have higher RMSD values than small proteins when an optimal alignment is reached. Recently, a logarithmic factor has been proposed to correct this size-dependency problem. This new measure is called RMSD100.