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Nadezhda Doncheva (Max Planck Institute for Informatics, Saarbruecken, Germany)The properties of individual amino acid residues contained in 3D protein structures are frequently studied for understanding structural and functional properties of proteins. Recent work showed that the topological centrality analysis of residue interaction networks derived from 3D protein structures allows the identification and interpretation of biologically important residues. Therefore, we developed the Cytoscape plugin RINalyzer, which supports simultaneous viewing and exploring the 2D network of interacting residues and the corresponding 3D protein structure. To this end, RINalyzer offers numerous visual analytics tools, including the computation and illustration of a comprehensive set of network topology measures for highlighting critical residues in the protein structure. RINalyzer’s network representation is especially useful for investigating the effect of residue mutations on protein structure and function, for instance, if the location of a mutated residue is distant from the affected active site.