F1000Research (Oct 2019)
An intrinsically disordered proteins community for ELIXIR [version 1; peer review: 2 approved]
- Norman E. Davey,
- M. Madan Babu,
- Martin Blackledge,
- Alan Bridge,
- Salvador Capella-Gutierrez,
- Zsuzsanna Dosztanyi,
- Rachel Drysdale,
- Richard J. Edwards,
- Arne Elofsson,
- Isabella C. Felli,
- Toby J. Gibson,
- Aleksandras Gutmanas,
- John M. Hancock,
- Jen Harrow,
- Desmond Higgins,
- Cy M. Jeffries,
- Philippe Le Mercier,
- Balint Mészáros,
- Marco Necci,
- Cedric Notredame,
- Sandra Orchard,
- Christos A. Ouzounis,
- Rita Pancsa,
- Elena Papaleo,
- Roberta Pierattelli,
- Damiano Piovesan,
- Vasilis J. Promponas,
- Patrick Ruch,
- Gabriella Rustici,
- Pedro Romero,
- Sirarat Sarntivijai,
- Gary Saunders,
- Benjamin Schuler,
- Malvika Sharan,
- Denis C. Shields,
- Joel L. Sussman,
- Jonathan A. Tedds,
- Peter Tompa,
- Michael Turewicz,
- Jiri Vondrasek,
- Wim F. Vranken,
- Bonnie Ann Wallace,
- Kanin Wichapong,
- Silvio C. E. Tosatto
Affiliations
- Norman E. Davey
- Division of Cancer Biology, Institute of Cancer Research, UK, London, SW3 6JB, UK
- M. Madan Babu
- MRC Laboratory of Molecular Biology,, Cambridge, CB2 0QH, UK
- Martin Blackledge
- Institut de Biologie Structurale, Université Grenoble Alpes, Grenoble, 38000, France
- Alan Bridge
- Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
- Salvador Capella-Gutierrez
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona, Spain
- Zsuzsanna Dosztanyi
- Department of Biochemistry, Eötvös Loránd University, Budapest, H-1117, Hungary
- Rachel Drysdale
- ELIXIR Hub, Wellcome Genome Campus, Cambridge, CB10 1SD, UK
- Richard J. Edwards
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
- Arne Elofsson
- Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm University, Stockholm, Sweden
- Isabella C. Felli
- Department of Chemistry and CERM “Ugo Schiff”, University of Florence, Florence, Italy
- Toby J. Gibson
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Aleksandras Gutmanas
- Protein Data Bank in Europe, European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Cambridge, CB10 1SD, UK
- John M. Hancock
- ELIXIR Hub, Wellcome Genome Campus, Cambridge, CB10 1SD, UK
- Jen Harrow
- ELIXIR Hub, Wellcome Genome Campus, Cambridge, CB10 1SD, UK
- Desmond Higgins
- Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Belfield, Dublin, D4, Ireland
- Cy M. Jeffries
- European Molecular Biology Laboratory, Hamburg, Germany
- Philippe Le Mercier
- Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
- Balint Mészáros
- Department of Biochemistry, Eötvös Loránd University, Budapest, H-1117, Hungary
- Marco Necci
- Department of Biomedical Sciences, University of Padua, Padua, Italy
- Cedric Notredame
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, 08003, Spain
- Sandra Orchard
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Cambridge, CB10 1SD, UK
- Christos A. Ouzounis
- BCPL-CPERI, Centre for Research & Technology Hellas (CERTH), Thessalonica, 57001, Greece
- Rita Pancsa
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, H-1117, Hungary
- Elena Papaleo
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, 2100, Denmark
- Roberta Pierattelli
- Department of Chemistry and CERM “Ugo Schiff”, University of Florence, Florence, Italy
- Damiano Piovesan
- Department of Biomedical Sciences, University of Padua, Padua, Italy
- Vasilis J. Promponas
- Bioinformatics Research Laboratory, Department of Biological Sciences, University of Cyprus, Nicosia, CY-1678, Cyprus
- Patrick Ruch
- HES-SO/HEG and SIB Text Mining, Swiss Institute of Bioinformatics, Geneva, Switzerland
- Gabriella Rustici
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
- Pedro Romero
- University of Wisconsin-Madison, Madison, WI, 53706-1544, USA
- Sirarat Sarntivijai
- ELIXIR Hub, Wellcome Genome Campus, Cambridge, CB10 1SD, UK
- Gary Saunders
- ELIXIR Hub, Wellcome Genome Campus, Cambridge, CB10 1SD, UK
- Benjamin Schuler
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
- Malvika Sharan
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Denis C. Shields
- Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Belfield, Dublin, D4, Ireland
- Joel L. Sussman
- Department of Structural Biology and the Israel Structural Proteomics, Center (ISPC), Weizmann Institute of Science, Reḥovot, 7610001, Israel
- Jonathan A. Tedds
- ELIXIR Hub, Wellcome Genome Campus, Cambridge, CB10 1SD, UK
- Peter Tompa
- VIB Center for Structural Biology (CSB), VIB Flemish Institute for Biotechnology, Brussels, 1050, Belgium
- Michael Turewicz
- Faculty of Medicine, Medizinisches Proteom-Center, Ruhr University Bochum, GesundheitsCampus 4, Bochum, 44801, Germany
- Jiri Vondrasek
- Institute of Organic Chemistry and Biochemistry, CAS, Prague, Czech Republic
- Wim F. Vranken
- VUB/ULB Interuniversity Institute of Bioinformatics in Brussels and Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, B-1050, Belgium
- Bonnie Ann Wallace
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, WC1H 0HA, UK
- Kanin Wichapong
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, The Netherlands
- Silvio C. E. Tosatto
- Department of Biomedical Sciences, University of Padua, Padua, Italy
- DOI
- https://doi.org/10.12688/f1000research.20136.1
- Journal volume & issue
-
Vol. 8
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.
