Influence of conservation on calculations of amino acid covariance in multiple sequence alignments

By Anthony Fodor, Richard W. Aldrich. 2004

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In Molecular Biology

Citations in the corpus

Protein 3D Structure Computed from Evolutionary Sequence Variation (2011, background): “This suggests that residue correlations could provide information about amino acid residues that are close in structure [4,5,6,7,8,9,10,11].”
Protein structure prediction from sequence variation (2012, methodology): “First, local statistical models do not deal with transitive correlations, and second, such models do not adequately take into account important information in conserved positions 33 .”
3D structures of membrane proteins from genomic sequencing (2012, neutral): “’’ Our ‘‘global’’ statistical approach is different from ‘‘local’’ approaches such as mutual information (MI) and variants thereof (Fodor and Aldrich, 2004; Livesay et al., 2012).”
Applications of sequence coevolution in membrane protein biochemistry (2017, unknown): “These results corroborate studies showing that reweighting of phylogeny and conservation in MI can improve predictions [52,60,61].”
Predicting Functionally Informative Mutations in Escherichia coli BamA Using Evolutionary Covariance Analysis (2013, methodology): “…pairs in the MI top 50 is not surprising: it has been established that covariance algorithms based on local statistical models act partly as conservation ﬁ lters, identifying covariance in a particular range of the entropy spectrum, which varies with the algorithm (Fodor and Aldrich 2004).”
Mutual information without the influence of phylogeny or entropy dramatically improves residue contact prediction (2008, methodology): “First, we measured the fraction of pairs in contact (non-hydrogen atom separations (cid:4) 6 A˚) as a function of rank order using a variety of methods: MI , MIr (Martin et al ., 2005), MIp , MIa , OMES (Fodor and Aldrich, 2004a) or McBASC (Fodor and Aldrich, 2004a).”
Quantitative Analysis of Hsp90-Client Interactions Reveals Principles of Substrate Recognition (2012, methodology): “…of Biochemistry, UT Southwestern, Dallas, TX 75390, USA 3Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA 4Howard Hughes Medical Institute, Cambridge, MA 02142, USA *Correspondence: lindquist_admin@wi.mit.edu http://dx.doi.org/10.1016/j.cell.2012.06.047”
Evolutionary information for specifying a protein fold (2005, methodology): “To examine this, we calculated sequence identities within core residues (3, 7, 20, 22, 33) between CC or IC sequences and natural WW domains.”
From Principal Component to Direct Coupling Analysis of Coevolution in Proteins: Low-Eigenvalue Modes are Needed for Structure Prediction (2012, unknown): “The direct use of correlations for discovering structural constraints such as residue-residue contacts in a protein fold has, unfortunately, remained of limited accuracy [5,6,9,11,13,16].”
Emerging methods in protein co-evolution (2013, methodology): “This method has been extensively tested and compared with newer methods and shows a small but significant capability to recover pairs of positions in physical contact 24 and still serves as a baseline to benchmark the performance of new methods 25 .”
3D Protein Structure Predicted from Sequence (2011, unknown): “This suggests that residue correlation can provide information about amino acid residues that are close in structure [4,5,6,7,8,9,10,11].”
MODELING AND INFERENCE OF SEQUENCE-STRUCTURE SPECIFICITY (2009, background): “Traditional residue coupling studies employ one of a number of possible statistical and information-theoretic metrics [6] to identify highly covarying residue pairs, and simply list all such pairs.”
Graphical Models of Residue Coupling in Protein Families (2008, background): “, mutual information or correlation, among many others [8]) is used to quantify the degree to which two residues in the family covary, presumably due to compensating mutations in the face of cooperativity.”
Protein Sectors: Statistical Coupling Analysis versus Conservation (2014, unknown): “12 2.5 Top eigenmode of the SCA matrix . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12”
Rewiring the specificity of two-component signal transduction systems. (2008, unknown): “To identify positions in this multiple sequence alignment that covary, we calculated the mutual information between each pair of sites (Atchley et al., 2000; Fodor and Aldrich, 2004) (Figures 1B and 1C).”