What's new (30/Aug/2013)
1. Protein-protein interaction (PPI) networks are available.
In the previous version, the knowledge described in IDEAL is limited to each of the IDPs. In this version, IDEAL empathizes the interaction of IDPs and their binding partners more explicitly, since it is quite important to understand IDPs in the context of a system and/or a PPI network. We regard each entry of IDEAL (protein) as a NODE, and an interaction of two entries (PPI) as an EDGE, preparing NODE pages as well as EDGE pages. The former contains the detailed information for an IDP, and the latter shows a complex form of the entry and its binding partner. Because NODE pages are connected by EDGE pages, and vice versa, users can easily walk around a PPI network by clicking these links. The birds-eye view of the PPI networks is also provided.
2. Redundant experimental data are clustered
Because the previous version simply enumerates experimental data of ordered/disordered regions, some entries showed a long list of redundant PDB entries. Then, we conducted clustering of PDB entries where similar sequences in a same binding mode are clustered in this version. Thus, the new IDEAL can present experimental data more concisely and informatively. The clustering results are also included in the IDEAL XML files.
3. NMR disorder is annotated in a systematic way
The IDRs were usually obtained by literature searches together with missing residues in the X-ray structures. Recently, we have developed a method to locate regions with large deviation among the NMR models that are almost equivalent to the missing residues in the X-ray structures . This version provides IDRs defined by this method, which are quite unique information available only in IDEAL.
4. IDR prediction by DICHOT
Although IDEAL presents experimental evidences, many users have requested us to include prediction results of ordered/disordered regions for reference. Thus, this version provides ordered/disordered prediction by the DICHOT system , together with domain assignments by HMM. Also, there is a link to the DICHOT server so that one can submit the amino acid sequence in interest to obtain a prediction result.
5. Other improvements
Acetylation and methylation sites are included in the list of post-translational modification sites. The ordered and disordered regions are shown in the sequence of the FASTA format with different colors.
1. M. Ota, et al. (2013) "An assignment of intrinsically disordered regions of proteins based on NMR structures." J. Struct. Biol., 181, 29-36.
2. S. Fukuchi, et al. (2009) "Development of an accurate classification system of proteins into structured and unstructured regions that uncovers novel structural domains: its application to human transcription factors." BMC Struct. Biol., 9, 26.