Intrinsically Disordered Protein (IDP) services

Name Description ELIXIR Node

This project addresses the limitations of current ontologies in capturing the dynamic nature of disordered protein regions by pursuing several primary objectives. Firstly, novel structural and functional ontologies will be developed to accurately represent the structural heterogeneity and dynamic functional annotations of proteins. These ontologies will incorporate timescales, annotating the kinetics of structural transformations to elucidate molecular mechanisms and regulatory pathways governing protein dynamics. 

Collaborating with existing databases and consortia will ensure seamless integration of ontological resources and experimental data, fostering interoperability and accelerating discoveries. A standardised file format specification will also be developed in collaboration with the Human Proteome Organisation Proteomics Standards Initiative, facilitating the encoding of structural state transitions within disordered protein regions. This specification will enhance data interoperability and exchange among research groups and databases, providing a common language for describing structural transitions and advancing our understanding of the functional implications of protein dynamics in biological systems.

 ELIXIR Belgium, ELIXIR Hungary, ELIXIR Italy, EMBL-EBI
ELIXIR Belgium, ELIXIR Cyprus, ELIXIR Czech Republic, ELIXIR Denmark, ELIXIR Estonia, ELIXIR Finland, ELIXIR France, ELIXIR Germany, ELIXIR Greece, ELIXIR Hungary, ELIXIR Ireland, ELIXIR Israel, ELIXIR Italy, ELIXIR Luxembourg, ELIXIR Netherlands, ELIXIR Norway, ELIXIR Portugal, ELIXIR Slovenia, ELIXIR Spain, ELIXIR Sweden, ELIXIR Switzerland, ELIXIR UK, EMBL-EBI
ELIXIR Belgium, ELIXIR Cyprus, ELIXIR Czech Republic, ELIXIR Denmark, ELIXIR Finland, ELIXIR France, ELIXIR Germany, ELIXIR Greece, ELIXIR Hungary, ELIXIR Israel, ELIXIR Italy, ELIXIR Netherlands, ELIXIR Norway, ELIXIR Portugal, ELIXIR Slovenia, ELIXIR Spain, ELIXIR Sweden, ELIXIR Switzerland, ELIXIR UK, EMBL-EBI
ELIXIR Italy
ELIXIR Italy
ELIXIR Italy

This project will deliver community-driven, FAIR and provenance-aware structural annotation workflows for PDBe-KB, an ELIXIR Core Data Resource (CDR). Through hackathons engaging IDP, proteomics and 3D-BioInfo communities, project participants will containerise key structural analysis tools as Nextflow modules. The resulting workflows will run on cloud, HPC or local environments and support public and sensitive datasets. The project strengthens ELIXIR’s structural biology infrastructure by expanding PDBe-KB’s computational ecosystem and enabling cross-domain annotation.

Predicted outcomes:

  • At least 15 containerised Nextflow modules created and documented
  • Three to five reproducible workflows integrated into PDBe-KB
  • Training materials, contributor guidelines and TeSS resources
  • Four hackathon-linked manuscripts plus an overarching community report
  • Five-year roadmap for future structural annotation needs
 EMBL-EBI, ELIXIR Spain, ELIXIR UK, ELIXIR Belgium, ELIXIR Czech Republic, ELIXIR Germany, ELIXIR Greece, ELIXIR Hungary, ELIXIR Israel, ELIXIR Italy, ELIXIR Norway, ELIXIR Sweden

FRET is a powerful technique for studying intrinsically disordered proteins (IDPs), yet FRET data are scattered across repositories and lack standardisation. This project will build the first FAIR-compliant central registry for IDP-FRET datasets and define MIADE-FRET, a minimum information standard for reporting these experiments. Together, they create a robust ecosystem for reusable structural data, enabling large-scale meta-analysis and training data for advanced computational models.

Predicted outcomes:

  • Central, FAIR-compliant public registry for IDP-FRET datasets
  • MIADE-FRET community reporting standard
  • Enhanced reproducibility and cross-study comparability
  • High-quality datasets for ML model development
  • Seamless integration with DisProt, MobiDB and PED, with long-term sustainability through ELIXIR Italy hosting
 ELIXIR Hungary, ELIXIR Portugal
ELIXIR France