Entropy correction eliminates major source of noise.

Raw and corrected contact score matrices for protein 1c9oA. The gray scale indicates the contact scores for each residue pair (i, j) for raw uncorrected scores computed from a Markov random field (MRF) model trained with persistent contrastive divergence (PCD) (A, Eq 2), average product corrected scores (B, Eq 17) and entropy corrected scores (C, Eq 18). The striping pattern in A arises from systematic score biases, which originate mainly from entropy.