Optimal data collection for correlated mutation analysis

Haim Ashkenazy, Ron Unger, Yossef Kliger

Research output: Contribution to journalArticlepeer-review

21 Scopus citations


The main objective of correlated mutation analysis (CMA) is to predict intra- protein residue-residue interactions from sequence alone. Despite considerable progress in algorithms and computer capabilities, the performance of CMA methods remains quite low. Here we examine whether, and to what extent, the quality of CMA methods depends on the sequences that are included in the multiple sequence alignment (MSA). The results revealed a strong correlation between the number of homologs in an MSA and CMA prediction strength. Furthermore, many of the current methods include only orthologs in the MSA, we found that it is beneficial to include both orthologs and paralogs in the MSA. Remarkably, even remote homologs contribute to the improved accuracy. Based on our findings we put forward an automated data collection procedure, with a minimal coverage of 50% between the query protein and its orthologs and paralogs. This procedure improves accuracy even in the absence of manual curation. In this era of massive sequencing and exploding sequence data, our results suggest that correlated mutation-based methods have not reached their inherent performance limitations and that the role of CMA in structural biology is far from being fulfilled.

Original languageEnglish
Pages (from-to)545-555
Number of pages11
JournalProteins: Structure, Function and Bioinformatics
Issue number3
StatePublished - 15 Feb 2009


  • Ab-initio structure prediction
  • Contact prediction
  • Correlated mutations
  • Protein structure prediction
  • Residue covariation


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