Open Access
Nucleic Acids Research, volume 44, issue W1, pages W367-W374
The RING 2.0 web server for high quality residue interaction networks
Publication type: Journal Article
Publication date: 2016-05-19
Journal:
Nucleic Acids Research
Quartile SCImago
Q1
Quartile WOS
Q1
Impact factor: 14.9
ISSN: 03051048, 13624962
PubMed ID:
27198219
Genetics
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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- We do not take into account publications that without a DOI.
- Statistics recalculated only for publications connected to researchers, organizations and labs registered on the platform.
- Statistics recalculated weekly.
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Piovesan D., Minervini G., Tosatto S. C. E. The RING 2.0 web server for high quality residue interaction networks // Nucleic Acids Research. 2016. Vol. 44. No. W1. p. W367-W374.
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Piovesan D., Minervini G., Tosatto S. C. E. The RING 2.0 web server for high quality residue interaction networks // Nucleic Acids Research. 2016. Vol. 44. No. W1. p. W367-W374.
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TY - JOUR
DO - 10.1093/nar/gkw315
UR - https://doi.org/10.1093%2Fnar%2Fgkw315
TI - The RING 2.0 web server for high quality residue interaction networks
T2 - Nucleic Acids Research
AU - Piovesan, Damiano
AU - Minervini, Giovanni
AU - Tosatto, S. C. E.
PY - 2016
DA - 2016/05/19 00:00:00
PB - Oxford University Press
SP - W367-W374
IS - W1
VL - 44
PMID - 27198219
SN - 0305-1048
SN - 1362-4962
ER -
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@article{2016_Piovesan,
author = {Damiano Piovesan and Giovanni Minervini and S. C. E. Tosatto},
title = {The RING 2.0 web server for high quality residue interaction networks},
journal = {Nucleic Acids Research},
year = {2016},
volume = {44},
publisher = {Oxford University Press},
month = {may},
url = {https://doi.org/10.1093%2Fnar%2Fgkw315},
number = {W1},
pages = {W367--W374},
doi = {10.1093/nar/gkw315}
}
Cite this
MLA
Copy
Piovesan, Damiano, et al. “The RING 2.0 web server for high quality residue interaction networks.” Nucleic Acids Research, vol. 44, no. W1, May. 2016, pp. W367-W374. https://doi.org/10.1093%2Fnar%2Fgkw315.