An intrinsically disordered proteins community for ELIXIR

Abstract

Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) are now recognised as major determinants in cellular regulation. This white paper presents a roadmap for future e-infrastructure developments in the field of IDP research within the ELIXIR framework. The goal of these developments is to drive the creation of high-quality tools and resources to support the identification, analysis and functional characterisation of IDPs. The roadmap is the result of a workshop titled “An intrinsically disordered protein user community proposal for ELIXIR” held at the University of Padua. The workshop, and further consultation with the members of the wider IDP community, identified the key priority areas for the roadmap including the development of standards for data annotation, storage and dissemination; integration of IDP data into the ELIXIR Core Data Resources; and the creation of benchmarking criteria for IDP-related software. Here, we discuss these areas of priority, how they can be implemented in cooperation with the ELIXIR platforms, and their connections to existing ELIXIR Communities and international consortia. The article provides a preliminary blueprint for an IDP Community in ELIXIR and is an appeal to identify and involve new stakeholders.

MobiDB: intrinsically disordered proteins in 2021

“…The objective of the new MobiDB (version 4) is to provide stable and sustainable access to data on disordered regions and proteins. As an ELIXIR resource, this is in line with the overall ELIXIR mission and complies with the goals described in the ELIXIR IDP community whitepaper ( 38 ). Sustainability has been improved primarily by optimizing the database schema, and by improving the update process and simplifying the data representation formats.…”

DichroWeb, a website for calculating protein secondary structure from circular dichroism spectroscopic data

“…In recent years there has been a growing interest in intrinsically disordered proteins (IDPs) and intrinsically‐disordered regions in proteins, which appear to be involved in important cellular processes such as control of the cell cycle, transcriptional activation, and signaling. 37 Structural studies of IDPs are challenging since they generally do not crystallize, and therefore there are very few entries in the PDB 38 which have large stretches or regions of disorder. Consequently, this type of protein is not represented in the current datasets that are publically available for empirical CD analyses.…”

DisProt in 2022: improved quality and accessibility of protein intrinsic disorder annotation

“…A number of DisProt annotations come from experiments performed under extreme conditions. These annotations, which were tagged as ambiguous in the previous DisProt version, are now described using the Minimum Information About Disorder Experiments (MIADE) guidelines ( https://www.psidev.info/groups/intrinsically-disordered-proteins ) ( 40 ). MIADE defines the minimal fundamental parameters that unambiguously characterize a disorder-related experiment.…”