Pairwise covariance adds little to secondary structure prediction but improves the prediction of non-canonical local structure

Background: Amino acid sequence probability distributions, or profiles, have been used successfully to predict secondary structure and local structure in proteins. Profile models assume the statistical independence of each position in the sequence, but the energetics of protein folding is better captured in a scoring function that is based on pairwise interactions, like a force field. Results: I-sites motifs are short sequence/structure motifs that populate the protein structure database due to energy-driven convergent evolution. Here we show that a pairwise covariant sequence model does not predict alpha helix or beta strand significantly better overall than a profile-based model, but it does improve the prediction of certain loop motifs. The finding is best explained by considering secondary structure profiles as multivariant, all-or-none models, which subsume covariant models. Pairwise covariance is nonetheless present and energetically rational. Examples of negative design are pre...

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: Christopher Bystroff, Bobbie-Jo M. Webb-Robertson
• Keywords: BMCBI 2008, Local Structure, Protein, Secondary Structure