Evidence map›Paper›PMID 31824649›Full record

ArticleF1000Research2019

An intrinsically disordered proteins community for ELIXIR.

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 and 34 more

Abstract read
In one paragraph

Article in F1000Research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.

0numbers the graph read from it
0cells of the map it votes in
10citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

10 citing papers in PubMed.

  1. Article
  2. Article
  3. Best practices for the manual curation of intrinsically disordered proteins in DisProt.Database : the journal of biological databases and curation · 2024
    Article
  4. Article
  5. Review
  6. Article
  7. Article
  8. Article
  9. Article
  10. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

44 authors.

Norman E DaveyDivision of Cancer Biology, Institute of Cancer Research, UK, London, SW3 6JB, UK.
M Madan BabuMRC Laboratory of Molecular Biology,, Cambridge, CB2 0QH, UK.
Martin BlackledgeInstitut de Biologie Structurale, Université Grenoble Alpes, Grenoble, 38000, France.
Alan BridgeSwiss-Prot Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland.
Salvador Capella-GutierrezLife Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona, Spain.ORCID 0000-0002-0309-604X
Zsuzsanna DosztanyiDepartment of Biochemistry, Eötvös Loránd University, Budapest, H-1117, Hungary.
Rachel DrysdaleELIXIR Hub, Wellcome Genome Campus, Cambridge, CB10 1SD, UK.
Richard J EdwardsSchool of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia.
Arne ElofssonDepartment of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm University, Stockholm, Sweden.ORCID 0000-0002-7115-9751
Isabella C FelliDepartment of Chemistry and CERM "Ugo Schiff", University of Florence, Florence, Italy.
Toby J GibsonStructural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
Aleksandras GutmanasProtein Data Bank in Europe, European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Cambridge, CB10 1SD, UK.ORCID 0000-0001-6311-0176
John M HancockELIXIR Hub, Wellcome Genome Campus, Cambridge, CB10 1SD, UK.ORCID 0000-0003-2991-2217
Jen HarrowELIXIR Hub, Wellcome Genome Campus, Cambridge, CB10 1SD, UK.
Desmond HigginsConway Institute of Biomolecular & Biomedical Research, University College Dublin, Belfield, Dublin, D4, Ireland.
Cy M JeffriesEuropean Molecular Biology Laboratory, Hamburg, Germany.
Philippe Le MercierSwiss-Prot Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland.ORCID 0000-0001-8528-090X
Balint MészárosDepartment of Biochemistry, Eötvös Loránd University, Budapest, H-1117, Hungary.
Marco NecciDepartment of Biomedical Sciences, University of Padua, Padua, Italy.
Cedric NotredameCentre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, 08003, Spain.
Sandra OrchardEuropean Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Cambridge, CB10 1SD, UK.ORCID 0000-0002-8878-3972
Christos A OuzounisBCPL-CPERI, Centre for Research & Technology Hellas (CERTH), Thessalonica, 57001, Greece.
Rita PancsaInstitute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, H-1117, Hungary.
Elena PapaleoComputational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, 2100, Denmark.
Roberta PierattelliDepartment of Chemistry and CERM "Ugo Schiff", University of Florence, Florence, Italy.ORCID 0000-0001-7755-0885
Damiano PiovesanDepartment of Biomedical Sciences, University of Padua, Padua, Italy.
Vasilis J PromponasBioinformatics Research Laboratory, Department of Biological Sciences, University of Cyprus, Nicosia, CY-1678, Cyprus.ORCID 0000-0003-3352-4831
Patrick RuchHES-SO/HEG and SIB Text Mining, Swiss Institute of Bioinformatics, Geneva, Switzerland.
Gabriella RusticiDepartment of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK.
Pedro RomeroUniversity of Wisconsin-Madison, Madison, WI, 53706-1544, USA.ORCID 0000-0002-6995-5193
Sirarat SarntivijaiELIXIR Hub, Wellcome Genome Campus, Cambridge, CB10 1SD, UK.
Gary SaundersELIXIR Hub, Wellcome Genome Campus, Cambridge, CB10 1SD, UK.
Benjamin SchulerDepartment of Biochemistry, University of Zurich, Zurich, Switzerland.
Malvika SharanStructural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
Denis C ShieldsConway Institute of Biomolecular & Biomedical Research, University College Dublin, Belfield, Dublin, D4, Ireland.
Joel L SussmanDepartment of Structural Biology and the Israel Structural Proteomics, Center (ISPC), Weizmann Institute of Science, Reḥovot, 7610001, Israel.
Jonathan A TeddsELIXIR Hub, Wellcome Genome Campus, Cambridge, CB10 1SD, UK.
Peter TompaVIB Center for Structural Biology (CSB), VIB Flemish Institute for Biotechnology, Brussels, 1050, Belgium.
Michael TurewiczFaculty of Medicine, Medizinisches Proteom-Center, Ruhr University Bochum, GesundheitsCampus 4, Bochum, 44801, Germany.ORCID 0000-0003-0737-1114
Jiri VondrasekInstitute of Organic Chemistry and Biochemistry, CAS, Prague, Czech Republic.
Wim F VrankenVUB/ULB Interuniversity Institute of Bioinformatics in Brussels and Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, B-1050, Belgium.
Bonnie Ann WallaceInstitute of Structural and Molecular Biology, Birkbeck College, University of London, London, WC1H 0HA, UK.
Kanin WichapongDepartment of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, The Netherlands.
Silvio C E TosattoDepartment of Biomedical Sciences, University of Padua, Padua, Italy.

Funding

UniProt - Text Mining and Large Language models to Enhance Functional Annotation in UniProt of Protein Variants Associated with Alzheimer's DiseaseU24HG007822 · NHGRI · GEORGETOWN UNIVERSITY · PI Alex Bateman, Alan James Bridge · 2018 to 2026
$53.0M
Medical Research Council MC_U105185859NHGRI NIH HHS U24 HG007822Wellcome Trust
6 · The paper itself

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.

Indexed as

Intrinsically Disordered ProteinsIntrinsically Disordered Proteinscellular regulationcommunity standardsdatabasesELIXIRintrinsically disordered proteinsprotein dynamicsprotein functionprotein-protein interactions

Identifiers

PMID31824649
PMCPMC6880265

What OpenQuestion holds

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.