Piovesan Damiano, Minervini Giovanni, Tosatto Silvio C E
Department of Biomedical Sciences, University of Padua, Padua 35121, Italy.
Department of Biomedical Sciences, University of Padua, Padua 35121, Italy CNR Institute of Neuroscience, Padua 35121, Italy
Nucleic Acids Res. 2016 Jul 8;44(W1):W367-74. doi: 10.1093/nar/gkw315. Epub 2016 May 19.
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.
残基相互作用网络（RINs）是表示蛋白质结构的另一种方式，其中节点是残基，弧是物理化学相互作用。RINs已被广泛且成功地用于分析突变效应、蛋白质折叠、结构域间通讯和催化活性。在此，我们展示RING 2.0，这是RING软件的新版本，用于识别蛋白质结构中的共价键和非共价键，包括π-π堆积和π-阳离子相互作用。RING 2.0速度极快，能生成包括溶剂和配体原子在内的链内和链间相互作用。由于对整个蛋白质数据库进行了复杂的距离阈值经验重新参数化，所生成的网络非常准确且可靠。默认情况下，RING输出是使用最优参数生成的，但网络服务器提供了一个详尽的界面来定制计算。该网络可以直接在浏览器中或Cytoscape中可视化。或者，用于Pymol的RING-Viz脚本允许在结构的原子水平上可视化相互作用。网络服务器和RING-Viz，以及广泛的帮助和教程，可从以下网址获取：http://protein.bio.unipd.it/ring 。
