Digested disorder

2015

Self Cite

This article continues an "Unreported Intrinsic Disorder in Proteins" series, the goal of which is to expose some interesting cases of missed (or overlooked, or ignored) disorder in proteins. The need for this series is justified by the observation that despite the fact that protein intrinsic disorder is widely accepted by the scientific community, there are still numerous instances when appreciation of this phenomenon is absent. This results in the avalanche of research papers which are talking about intrinsically disordered proteins (or hybrid proteins with ordered and disordered regions) not recognizing that they are talking about such proteins. Articles in the "Unreported Intrinsic Disorder in Proteins" series provide a fast fix for some of the recent noticeable disorder overlooks.

Section: Introductionmentioning

confidence: 98%

Unreported intrinsic disorder in proteins: Disorder emergency room

2015

Self Cite

Quarterly intrinsic disorder digest (January-February-March, 2014)

DeForte

Reddy

2016

Self Cite

This is the 5 th issue of the Digested Disorder series that represents a reader's digest of the scientific literature on intrinsically disordered proteins. We continue to use only 2 criteria for inclusion of a paper to this digest: The publication date (a paper should be published within the covered time frame) and the topic (a paper should be dedicated to any aspect of protein intrinsic disorder). The current digest issue covers papers published during the first quarter of 2014; i.e., during the period of January, February, and March of 2014. Similar to previous issues, the papers are grouped hierarchically by topics they cover, and for each of the included papers a short description is given on its major findings. The goal of this series is to provide an unbiased and condensed survey of the literature on intrinsically disordered proteins on a quarterly basis. As in the previous issues, no special filtering was used except to verify the print date, and exclude those papers not related to the topic. The digest article is structured hierarchically and papers are grouped in several sections: (1) structures of intrinsically disordered proteins (IDPs); (2) functions of IDPs; (3) methods for the IDP analysis; (4) proteomics of IDPs; (5) IDPs and diseases; and (6) IDPs/IDPRs as drugs or drug targets. One should keep in mind that the unambiguous classification of many papers is challenged by the intertwining of the topics they cover.In the 5 th digest of this series, we cover papers published in January, February, and March of 2014. We used the following search term in PubMed: (intrinsically OR natively OR naturally OR inherently) AND (disordered OR unfolded OR unstructured OR denatured) AND (protein OR region OR peptide OR domain) AND ("2014/01" [PPDAT]: "2014/ 03"[PPDAT]), which returned 103 hits. After filtering hits not relevant to the topic, we have covered 94 articles here. Figure 1 represents a word cloud, which shows the most represented words from all the abstracts of papers included in this issue.We also introduce below a new rubric "Spotlight" that specifically emphasize some of the most interesting and important developments in the field of intrinsically disordered proteins during the covered quarter. Spotlight: IDP databases and the rise of the ensemble viewDatabases of experimentally verified IDPs are critical for the development of tools that predict intrinsic disorder, and provide an important data set for the study of IDP functions, motifs and structural behavior. One of the first databases to provide experimental evidence of intrinsic disorder was oddly enough, the Protein Data Bank, where regions of missing electron density in x-ray crystal structures provide an indication of possible disorder. The major databases for IDPs are Disprot 5 and the recently updated IDEAL 6 and the mostly predictor based databases d2p2 7 and MobiDB.8 CONTACT Vladimir N. Uversky

Quarterly intrinsic disorder digest (April–May–June, 2014)

DeForte

2017

Self Cite

This is the 6 th issue of the Digested Disorder series that continues to use only 2 criteria for inclusion of a paper to this digest: The publication date (a paper should be published within the covered time frame) and the topic (a paper should be dedicated to any aspect of protein intrinsic disorder). The current digest issue covers papers published during the second quarter of 2014; i.e., during the period of April, May, and June of 2014. Similar to previous issues, the papers are grouped hierarchically by topics they cover, and for each of the included papers a short description is given on its major findings.