A Shannon entropy-based filter detects high-quality profile-profile alignments in searches for remote homologues

Detection of homologous proteins with low-sequence identity to a given target (remote homologues) is routinely performed with alignment algorithms that take advantage of sequence profile. In this article, we investigate the efficacy of differ- ent alignment procedures for the task at hand on a set of 185 protein pairs with similar structures but low-sequence similarity. Criteria based on the SCOP label detection and MaxSub scores are adopted to score the results. We investigate the efficacy of alignments based on sequence-sequence, sequence- profile, and profile-profile information. We confirm that with profile-profile alignments the results are better than with other procedures. In addition, we report, and this is novel, that the selection of the results of the profile-profile alignments can be im- proved by using Shannon entropy, indicating that this parameter is important to recognize good pro- file-profile alignments among a plethora of meaning- less pairs. By this, we enhance the global search accuracy without losing sensitivity and filter out most of the erroneous alignments. We also show that when the entropy filtering is adopted, the quality of the resulting alignments is comparable to that com- puted for the target and template structures with CE, a structural alignment program. Proteins 2004