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F1000Res. 2019 Oct 15;8. pii: ELIXIR-1753. doi: 10.12688/f1000research.20136.1. eCollection 2019.

An intrinsically disordered proteins community for ELIXIR.

Author information

1
Division of Cancer Biology, Institute of Cancer Research, UK, London, SW3 6JB, UK.
2
MRC Laboratory of Molecular Biology,, Cambridge, CB2 0QH, UK.
3
Institut de Biologie Structurale, Université Grenoble Alpes, Grenoble, 38000, France.
4
Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland.
5
Life Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona, Spain.
6
Department of Biochemistry, Eötvös Loránd University, Budapest, H-1117, Hungary.
7
ELIXIR Hub, Wellcome Genome Campus, Cambridge, CB10 1SD, UK.
8
School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia.
9
Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm University, Stockholm, Sweden.
10
Department of Chemistry and CERM "Ugo Schiff", University of Florence, Florence, Italy.
11
Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
12
Protein Data Bank in Europe, European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Cambridge, CB10 1SD, UK.
13
Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Belfield, Dublin, D4, Ireland.
14
European Molecular Biology Laboratory, Hamburg, Germany.
15
Department of Biomedical Sciences, University of Padua, Padua, Italy.
16
Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, 08003, Spain.
17
Universitat Pompeu Fabra (UPF), Barcelona, Spain.
18
European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Cambridge, CB10 1SD, UK.
19
BCPL-CPERI, Centre for Research & Technology Hellas (CERTH), Thessalonica, 57001, Greece.
20
Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, H-1117, Hungary.
21
Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, 2100, Denmark.
22
Bioinformatics Research Laboratory, Department of Biological Sciences, University of Cyprus, Nicosia, CY-1678, Cyprus.
23
HES-SO/HEG and SIB Text Mining, Swiss Institute of Bioinformatics, Geneva, Switzerland.
24
Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK.
25
University of Wisconsin-Madison, Madison, WI, 53706-1544, USA.
26
Department of Biochemistry, University of Zurich, Zurich, Switzerland.
27
Department of Structural Biology and the Israel Structural Proteomics, Center (ISPC), Weizmann Institute of Science, Reḥovot, 7610001, Israel.
28
VIB Center for Structural Biology (CSB), VIB Flemish Institute for Biotechnology, Brussels, 1050, Belgium.
29
Faculty of Medicine, Medizinisches Proteom-Center, Ruhr University Bochum, GesundheitsCampus 4, Bochum, 44801, Germany.
30
Institute of Organic Chemistry and Biochemistry, CAS, Prague, Czech Republic.
31
VUB/ULB Interuniversity Institute of Bioinformatics in Brussels and Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, B-1050, Belgium.
32
Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, WC1H 0HA, UK.
33
Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, The Netherlands.

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.

KEYWORDS:

ELIXIR; cellular regulation; community standards; databases; intrinsically disordered proteins; protein dynamics; protein function; protein-protein interactions

PMID:
31824649
PMCID:
PMC6880265
DOI:
10.12688/f1000research.20136.1
[Indexed for MEDLINE]
Free PMC Article

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