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Nucleic Acids Res. 2014 Jan;42(Database issue):D320-5. doi: 10.1093/nar/gkt1010. Epub 2013 Oct 30.

IDEAL in 2014 illustrates interaction networks composed of intrinsically disordered proteins and their binding partners.

Author information

1
Faculty of Engineering, Maebashi Institute of Technology, Maebashi 371-0816, Japan, Graduate School of Information Science, Nagoya University, Nagoya 464-8601, Japan, HOLONICS Corporation, Numazu 411-0803, Japan and Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya 464-8601, Japan.

Abstract

IDEAL (Intrinsically Disordered proteins with Extensive Annotations and Literature, http://www.ideal.force.cs.is.nagoya-u.ac.jp/IDEAL/) is a collection of intrinsically disordered proteins (IDPs) that cannot adopt stable globular structures under physiological conditions. Since its previous publication in 2012, the number of entries in IDEAL has almost tripled (120 to 340). In addition to the increase in quantity, the quality of IDEAL has been significantly improved. The new IDEAL incorporates the interactions of IDPs and their binding partners more explicitly, and illustrates the protein-protein interaction (PPI) networks and the structures of protein complexes. Redundant experimental data are arranged based on the clustering of Protein Data Bank entries, and similar sequences with the same binding mode are grouped. As a result, the new IDEAL presents more concise and informative experimental data. Nuclear magnetic resonance (NMR) disorder is annotated in a systematic manner, by identifying the regions with large deviations among the NMR models. The ordered/disordered and new domain predictions by DICHOT are available, as well as the domain assignments by HMMER. Some examples of the PPI networks and the highly deviated regions derived from NMR models will be described, together with other advances. These enhancements will facilitate deeper understanding of IDPs, in terms of their flexibility, plasticity and promiscuity.

PMID:
24178034
PMCID:
PMC3965115
DOI:
10.1093/nar/gkt1010
[Indexed for MEDLINE]
Free PMC Article

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