Effectiveness of correlation analysis in identifying protein residues undergoing correlated evolution.

By D. Pollock, William R. Taylor. 1997

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Citations in the corpus

Learning generative models for protein fold families (2011, background): “One limitation associated with a sequence-only approach to learning a statistical model for a domain family is that the correlations observed in the MSA can be inﬂated due to phylogeny [37, 38].”
Graphical Models of Residue Coupling in Protein Families (2008, background): “Phylogeny can play a significant role in observed sequence covariation [28], [30].”
An Evolutionary-Network Model Reveals Stratified Interactions in the V3 Loop of the HIV-1 Envelope (2007, background): “However, it is well known that shared ancestry will produce spurious correlations between jointly inherited character states [31,32].”
De Novo Structure Prediction of Globular Proteins Aided by Sequence Variation-Derived Contacts (2014, background): “For some time now, the importance of residue-residue contacts in protein structure prediction has been known and explored [1,2,3,4].”
Graphical models of residue coupling in protein families (2005, background): “Phylogeny can play a significant role in observed sequence covariation [28], [30].”
Co-evolving residues in membrane proteins (2007, methodology): “…most commonly used relies on the calculation of a Pearson correlation coefficient to detect alignment positions with similar patterns of amino acid change (Gobel et al., 1994; Kundrotas and Alexov, 2006; Neher, 1994; Olmea and Valencia, 1997; Pollock and Taylor, 1997; Taylor and Hatrick, 1994).”
Finding and Leveraging Structure in Learning Problems (2012, background): “One limitation associated with a sequence-only approach to learning a statistical model for a domain family is that the correlations observed in the MSA can be inflated due to phylogeny [73, 154].”
Using multiple interdependency to separate functional from phylogenetic correlations in protein alignments (2003, background): “Several studies have demonstrated the difficulty in distinguishing covariations stemming from functional biological interactions between amino acids from the background covariation due to phylogenetic relationships (Pollock and Taylor, 1997).”