title: IDEAL in 2014 illustrates interaction networks composed of intrinsically disordered proteins and their binding partners.
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.
authors.affiliation: 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.
authors.forename: Satoshi
authors.initials: S
authors.lastname: Fukuchi
authors.forename: Takayuki
authors.initials: T
authors.lastname: Amemiya
authors.forename: Shigetaka
authors.initials: S
authors.lastname: Sakamoto
authors.forename: Yukiko
authors.initials: Y
authors.lastname: Nobe
authors.forename: Kazuo
authors.initials: K
authors.lastname: Hosoda
authors.forename: Yumiko
authors.initials: Y
authors.lastname: Kado
authors.forename: Seiko D
authors.initials: SD
authors.lastname: Murakami
authors.forename: Ryotaro
authors.initials: R
authors.lastname: Koike
authors.forename: Hidekazu
authors.initials: H
authors.lastname: Hiroaki
authors.forename: Motonori
authors.initials: M
authors.lastname: Ota
mesh_terms: D030562:Databases, Protein; D020407:Internet; D064267:Intrinsically Disordered Proteins / Q000737:chemistry* / Q000378:metabolism*; D019906:Nuclear Magnetic Resonance, Biomolecular; D060066:Protein Interaction Maps
chemical_list: D064267:Intrinsically Disordered Proteins