Inference of direct residue contacts in two-component signaling.

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Dissecting the Specificity of Protein-Protein Interaction in Bacterial Two-Component Signaling: Orphans and Crosstalks (2011, methodology): “DCA is based on the co-evolution of inter-protein contact residues.”
Structural basis of histidine kinase autophosphorylation deduced by integrating genomics, molecular dynamics, and mutagenesis (2012, methodology): “It is precisely for this purpose that we developed a computational-biology approach termed direct coupling analysis (DCA) (11, 12) with the ability to extract residue–residue contacts for individual proteins or protein interaction partners from the sequence variability in extensive protein family da”
Toward rationally redesigning bacterial two-component signaling systems using coevolutionary information (2014, methodology): “The recent development of a global statistical inference method called direct coupling analysis (DCA) (17, 18, 23) has advanced the study of sequence coevolution by pruning out the contributions from indirect couplings (i.e., statistical couplings through third party residues or phylogenetic…”