Correlated mutations in models of protein sequences: phylogenetic and structural effects

By A. Lapedes, B. Giraud, L. Liu, Gary D. Stormo. 1999

Subfields: Computational Biology & Bioinformatics

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Citations in the corpus

Protein 3D Structure Computed from Evolutionary Sequence Variation (2011, methodology): “[14,15] and then implemented algorithmically using belief propagation to infer residue-residue interactions in protein-protein interfaces by Weigt et al.”
Robust and accurate prediction of residue–residue interactions across protein interfaces using evolutionary information (2014, background): “As noted above, the accuracy of these models is reduced by the confounding of direct and indirect correlations ( Lapedes et al., 1999 ; Weigt et al., 2009 ); the application of global statistical models to coevolution-based contact prediction across interfaces has been limited to the case of the…”
Protein sectors: evolutionary units of three-dimensional structure (2009, neutral): “One possible interpretation of this result is that covariation analyses fail to capture the essential design of proteins (Fodor and Aldrich, 2004), but, consistent with other studies (Kass and Horovitz, 2002; Lapedes et al., 1999; Lichtarge et al., 1996), the sector hypothesis suggests an alternate ”
Improved Contact Predictions Using the Recognition of Protein Like Contact Patterns (2014, methodology): “The introduction of predictors using global models, inferring couplings between residues from the observed correlations, significantly increases the accuracy of co-variation based methods [12-16].”
Fast and Accurate Multivariate Gaussian Modeling of Protein Families: Predicting Residue Contacts and Protein-Interaction Partners (2014, background): “Proposed initially more than a decade ago [21,22], it was not until very recently that the first successful MaxEnt approaches to the study of co-evolution were published [8,23].”
Transformer protein language models are unsupervised structure learners (2020, methodology): “This was proposed by Lapedes et al. (1999) and reintroduced by Thomas et al.”
Predicting Functionally Informative Mutations in Escherichia coli BamA Using Evolutionary Covariance Analysis (2013, background): “These transitive correlations can extend beyond three positions, creating large, nonspeci ﬁ c networks of correlated residues (Lapedes et al. 1999).”
Fast pseudolikelihood maximization for direct-coupling analysis of protein structure from many homologous amino-acid sequences (2014, methodology): “The method of Lapedes et al [19] has not been evaluated again using modern data and modern computer resources, and its relative performance as to prediction accuracy is hence unknown.”
Inferring interaction partners from protein sequences (2016, background): “In particular, the maximum entropy principle [8] specifies the least-structured global statistical model consistent with the one- and two-point statistics of an alignment [5].”