Question

In Grid representation, in a translational scan the mobile molecule B moves through the grid representing the static molecule A and a signal describing shape complementarity, fc, is generated for each mapping. Mathematically the correlation function, fc, of fA and fB is given by ______ where N is the number of grid points along the cubic axes i, j, and k and α, β, and γ are the translational vectors of the mobile molecule B relative to the static one A.

(a) fc = \(\sum_{i=1,j=1,k=1}^N\) (fA,i,j,k * fBi+αj+βk+ɣ)

(b) fc = \(\sum_{i=0,j=0,k=0}^N\) (fA,i,j,k * fBi+αj+βk+ɣ)

(c) fc = \(\sum_{i=1,j=1,k=1}^N\) (fA,0,0,0 * fBi+αj+βk+ɣ)

(d) fc = \(\sum_{i=0,j=0,k=0}^N\) (f0,i,j,k * fBi+αj+βk+ɣ)

The question was asked during a job interview.

The query is from Molecular Complementarity in section Predicting the Structure of Protein – Biomolecular Interactions of Bioinformatics

Answer 1

The correct option is (a) fc = \(\sum_{i=1,j=1,k=1}^N\) (fA,i,j,k * fBi+αj+βk+ɣ)

To explain I would say: The overlap between points representing the surface of the molecules is scored favorably, however, overlap with points representing the core of the static molecule are scored unfavorably. Zero correlation score is given to two molecules not in contact. Negative scores represent surface overlap with the core region of molecule A.