Databases for intrinsically disordered proteins

Abstract

Intrinsically disordered regions (IDRs) lacking a fixed three-dimensional protein structure are widespread and play a central role in cell regulation. Only a small fraction of IDRs have been functionally characterized, with heterogeneous experimental evidence that is largely buried in the literature. Predictions of IDRs are still difficult to estimate and are poorly characterized. Here, an overview of the publicly available knowledge about IDRs is reported, including manually curated resources, deposition databases and prediction repositories. The types, scopes and availability of the various resources are analyzed, and their complementarity and overlap are highlighted. The volume of information included and the relevance to the field of structural biology are compared.

Keywords: databases; flexible proteins; intrinsically disordered proteins; protein ensembles.

Figure 1

Overview of IDP/IDR data and the respective databases. The databases are organized according to the type of IDP/IDR data stored: sequence, binding regions and structural data. In the top part, examples are shown for each category using part of the N-terminal region of the human p53 protein (UniProtID p04637), its MDM2-binding short linear motif (ELM accession ELME000184 and PDB entry 1ycr, chain B, red) and the corresponding structural ensemble (PED ID PED00037e000). Curated databases are indicated with a check mark, deposition databases with a database icon and databases with predicted data with a machine-learning icon. Databases aggregating data from different sources have a light blue background. Created with BioRender (https://biorender.com/).