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. 2016 Jul 8;44(W1):W367-74.
doi: 10.1093/nar/gkw315. Epub 2016 May 19.

The RING 2.0 web server for high quality residue interaction networks

Affiliations

The RING 2.0 web server for high quality residue interaction networks

Damiano Piovesan et al. Nucleic Acids Res. .

Abstract

Residue interaction networks (RINs) are an alternative way of representing protein structures where nodes are residues and arcs physico-chemical interactions. RINs have been extensively and successfully used for analysing mutation effects, protein folding, domain-domain communication and catalytic activity. Here we present RING 2.0, a new version of the RING software for the identification of covalent and non-covalent bonds in protein structures, including π-π stacking and π-cation interactions. RING 2.0 is extremely fast and generates both intra and inter-chain interactions including solvent and ligand atoms. The generated networks are very accurate and reliable thanks to a complex empirical re-parameterization of distance thresholds performed on the entire Protein Data Bank. By default, RING output is generated with optimal parameters but the web server provides an exhaustive interface to customize the calculation. The network can be visualized directly in the browser or in Cytoscape. Alternatively, the RING-Viz script for Pymol allows visualizing the interactions at atomic level in the structure. The web server and RING-Viz, together with an extensive help and tutorial, are available from URL: http://protein.bio.unipd.it/ring.

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Figures

Figure 1.
Figure 1.
Orientation definition in RING. π–π stacking interactions adopt parallel (P), normal (N), lateral (L), tilted edge to face (T-EF) and tilted face to edge (T-FE) orientations. Orientation in π–cation interactions is provided only for contacts involving arginine and describes guanidine plane positioning relative to the partner ring and it is limited to P, L and N conformations.
Figure 2.
Figure 2.
Distance distribution for the six different interaction types. Hydrogen bonds are split into side chain (SC) and main chain (MC). Ionic interactions are characterized by the positively charged residue. Van der Waals interaction by secondary structure of the pair (E = sheet, H = helix, x = undefined). π–π stacking and π–cation interactions are separated by orientation type (see ‘Materials and Methods’ section). Red and blue vertical lines correspond respectively to the ‘strict’ and ‘relaxed’ thresholds in the web server.
Figure 3.
Figure 3.
RING result page for the human p27Kip kinase inhibitory domain bound to the phosphorylated cyclinA-Cdk2 complex (PDB code: 1JSU). The top-left graph shows the RIN with nodes and edges coloured according to the legend in the top right part. Highlighted interactions are shown in the lateral panels (structures in cartoon representation, interacting residues as sticks) and have been generated using the RING-Viz script (see ‘Materials and Methods’ section). The three inserts represent the same network graph with different colouring schemes. Clockwise from the top-right corner, the highlighted node attributes are: mutual information, conservation and node degree.

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