An intrinsically disordered proteins community for ELIXIR

. 2019 ; 8 () : . [epub] 20191015

Jazyk angličtina Země Velká Británie, Anglie Médium electronic-ecollection

Typ dokumentu časopisecké články, Research Support, N.I.H., Extramural, práce podpořená grantem

Perzistentní odkaz   https://www.medvik.cz/link/pmid31824649

Grantová podpora
Wellcome Trust - United Kingdom
MC_U105185859 Medical Research Council - United Kingdom
U24 HG007822 NHGRI NIH HHS - United States

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.

BCPL CPERI Centre for Research and Technology Hellas Thessalonica 57001 Greece

Bioinformatics Research Laboratory Department of Biological Sciences University of Cyprus Nicosia CY 1678 Cyprus

Centre for Genomic Regulation The Barcelona Institute of Science and Technology Barcelona 08003 Spain

Computational Biology Laboratory Danish Cancer Society Research Center Copenhagen 2100 Denmark

Conway Institute of Biomolecular and Biomedical Research University College Dublin Belfield Dublin D4 Ireland

Department of Biochemistry and Biophysics and Science for Life Laboratory Stockholm University Stockholm Sweden

Department of Biochemistry Cardiovascular Research Institute Maastricht Maastricht University Maastricht The Netherlands

Department of Biochemistry Eötvös Loránd University Budapest H 1117 Hungary

Department of Biochemistry University of Zurich Zurich Switzerland

Department of Biomedical Sciences University of Padua Padua Italy

Department of Chemistry and CERM Ugo Schiff University of Florence Florence Italy

Department of Genetics University of Cambridge Cambridge CB2 3EH UK

Department of Structural Biology and the Israel Structural Proteomics Center Weizmann Institute of Science Reḥovot 7610001 Israel

Division of Cancer Biology Institute of Cancer Research UK London SW3 6JB UK

ELIXIR Hub Wellcome Genome Campus Cambridge CB10 1SD UK

European Bioinformatics Institute European Molecular Biology Laboratory Cambridge CB10 1SD UK

European Molecular Biology Laboratory Hamburg Germany

Faculty of Medicine Medizinisches Proteom Center Ruhr University Bochum GesundheitsCampus 4 Bochum 44801 Germany

HES SO HEG and SIB Text Mining Swiss Institute of Bioinformatics Geneva Switzerland

Institut de Biologie Structurale Université Grenoble Alpes Grenoble 38000 France

Institute of Enzymology Research Centre for Natural Sciences of the Hungarian Academy of Sciences Budapest H 1117 Hungary

Institute of Organic Chemistry and Biochemistry CAS Prague Czech Republic

Institute of Structural and Molecular Biology Birkbeck College University of London London WC1H 0HA UK

Life Sciences Department Barcelona Supercomputing Center Barcelona Spain

MRC Laboratory of Molecular Biology Cambridge CB2 0QH UK

Protein Data Bank in Europe European Bioinformatics Institute European Molecular Biology Laboratory Cambridge CB10 1SD UK

School of Biotechnology and Biomolecular Sciences University of New South Wales Sydney NSW Australia

Structural and Computational Biology Unit European Molecular Biology Laboratory Heidelberg Germany

Swiss Prot Group SIB Swiss Institute of Bioinformatics Geneva Switzerland

Universitat Pompeu Fabra Barcelona Spain

University of Wisconsin Madison Madison WI 53706 1544 USA

VIB Center for Structural Biology VIB Flemish Institute for Biotechnology Brussels 1050 Belgium

VUB ULB Interuniversity Institute of Bioinformatics in Brussels and Structural Biology Brussels Vrije Universiteit Brussel Brussels B 1050 Belgium

Zobrazit více v PubMed

Babu MM, Kriwacki RW, Pappu RV: Structural biology. Versatility from protein disorder. PubMed DOI

Baggett DW, Nath A: The Rational Discovery of a Tau Aggregation Inhibitor. PubMed DOI PMC

Bah A, Forman-Kay JD: Modulation of Intrinsically Disordered Protein Function by Post-translational Modifications. PubMed DOI PMC

Beltrao P, Albanèse V, Kenner LR, et al. : Systematic functional prioritization of protein posttranslational modifications. PubMed DOI PMC

Bernadó P, Mylonas E, Petoukhov MV, et al. : Structural characterization of flexible proteins using small-angle X-ray scattering. PubMed DOI

Best RB: Computational and theoretical advances in studies of intrinsically disordered proteins. PubMed DOI

Blikstad C, Ivarsson Y: High-throughput methods for identification of protein-protein interactions involving short linear motifs. PubMed DOI PMC

Bonetti D, Troilo F, Brunori M, et al. : How Robust Is the Mechanism of Folding-Upon-Binding for an Intrinsically Disordered Protein? PubMed DOI PMC

Borgia A, Borgia MB, Bugge K, et al. : Extreme disorder in an ultrahigh-affinity protein complex. PubMed DOI PMC

Britan A, Cusin I, Hinard V, et al. : Accelerating annotation of articles via automated approaches: evaluation of the neXtA PubMed DOI PMC

Buljan M, Chalancon G, Eustermann S, et al. : Tissue-specific splicing of disordered segments that embed binding motifs rewires protein interaction networks. PubMed DOI PMC

Camilloni C, De Simone A, Vranken WF, et al. : Determination of secondary structure populations in disordered states of proteins using nuclear magnetic resonance chemical shifts. PubMed DOI

Chong SH, Chatterjee P, Ham S: Computer Simulations of Intrinsically Disordered Proteins. PubMed DOI

Chouard T: Structural biology: Breaking the protein rules. PubMed DOI

Cilia E, Pancsa R, Tompa P, et al. : The DynaMine webserver: predicting protein dynamics from sequence. PubMed DOI PMC

Corbi-Verge C, Kim PM: Motif mediated protein-protein interactions as drug targets. PubMed DOI PMC

Csizmok V, Forman-Kay JD: Complex regulatory mechanisms mediated by the interplay of multiple post-translational modifications. PubMed DOI

Davey NE: The functional importance of structure in unstructured protein regions. PubMed DOI

Davey NE, Cyert MS, Moses AM: Short linear motifs - PubMed DOI PMC

Davey NE, Morgan DO: Building a Regulatory Network with Short Linear Sequence Motifs: Lessons from the Degrons of the Anaphase-Promoting Complex. PubMed DOI PMC

Davey NE, Seo MH, Yadav VK, et al. : Discovery of short linear motif-mediated interactions through phage display of intrinsically disordered regions of the human proteome. PubMed DOI

Davey NE, Travé G, Gibson TJ: How viruses hijack cell regulation. PubMed DOI

Dosztányi Z, Csizmók V, Tompa P, et al. : The pairwise energy content estimated from amino acid composition discriminates between folded and intrinsically unstructured proteins. PubMed DOI

Dosztányi Z, Mészáros B, Simon I: ANCHOR: web server for predicting protein binding regions in disordered proteins. PubMed DOI PMC

Dunker AK, Silman I, Uversky VN, et al. : Function and structure of inherently disordered proteins. PubMed DOI

Durinx C, McEntyre J, Appel R, et al. : Identifying ELIXIR core data resources [version 2; peer review: 2 approved]. PubMed DOI PMC

Dyson HJ, Wright PE: How do intrinsically disordered viral proteins hijack the cell? PubMed DOI PMC

Dyson HJ, Wright PE: Intrinsically unstructured proteins and their functions. PubMed DOI

Edwards RJ, Palopoli N: Computational prediction of short linear motifs from protein sequences. PubMed DOI

Felli IC, Pierattelli R: Intrinsically Disordered Proteins Studied by NMR Spectroscopy.Springer.2015. 10.1007/978-3-319-20164-1 DOI

Forman-Kay JD, Mittag T: From sequence and forces to structure, function, and evolution of intrinsically disordered proteins. PubMed DOI PMC

Franke D, Petoukhov MV, Konarev PV, et al. : PubMed DOI PMC

Fuertes G, Banterle N, Ruff KM, et al. : Decoupling of size and shape fluctuations in heteropolymeric sequences reconciles discrepancies in SAXS vs. FRET measurements. PubMed DOI PMC

Fuxreiter M: Fold or not to fold upon binding - does it really matter? PubMed DOI

Gibson TJ, Dinkel H, Van Roey K, et al. : Experimental detection of short regulatory motifs in eukaryotic proteins: tips for good practice as well as for bad. PubMed DOI PMC

Gouw M, Michael S, Sámano-Sánchez H, et al. : The eukaryotic linear motif resource - 2018 update. PubMed DOI PMC

Guharoy M, Bhowmick P, Sallam M, et al. : Tripartite degrons confer diversity and specificity on regulated protein degradation in the ubiquitin-proteasome system. PubMed DOI PMC

Hess B, Kutzner C, van der Spoel D, et al. : GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. PubMed DOI

Holehouse AS, Pappu RV: Collapse Transitions of Proteins and the Interplay Among Backbone, Sidechain, and Solvent Interactions. PubMed DOI PMC

Holmstrom ED, Holla A, Zheng W, et al. : Accurate Transfer Efficiencies, Distance Distributions, and Ensembles of Unfolded and Intrinsically Disordered Proteins From Single-Molecule FRET. PubMed DOI PMC

Huang J, MacKerell AD, Jr: Force field development and simulations of intrinsically disordered proteins. PubMed DOI PMC

Iakoucheva LM, Radivojac P, Brown CJ, et al. : The importance of intrinsic disorder for protein phosphorylation. PubMed DOI PMC

Iešmantavicius V, Dogan J, Jemth P, et al. : Helical propensity in an intrinsically disordered protein accelerates ligand binding. PubMed DOI

Ivarsson Y, Jemth P: Affinity and specificity of motif-based protein-protein interactions. PubMed DOI

Kriwacki RW, Hengst L, Tennant L, et al. : Structural studies of p21Waf1/Cip1/Sdi1 in the free and Cdk2-bound state: conformational disorder mediates binding diversity. PubMed DOI PMC

Kruse T, Biedenkopf N, Hertz EPT, et al. : The Ebola Virus Nucleoprotein Recruits the Host PP2A-B56 Phosphatase to Activate Transcriptional Support Activity of VP30. PubMed DOI

Krystkowiak I, Davey NE: SLiMSearch: a framework for proteome-wide discovery and annotation of functional modules in intrinsically disordered regions. PubMed DOI PMC

Light S, Sagit R, Sachenkova O, et al. : Protein expansion is primarily due to indels in intrinsically disordered regions. PubMed DOI

Martin EW, Mittag T: Relationship of Sequence and Phase Separation in Protein Low-Complexity Regions. PubMed DOI PMC

Mészáros B, Kumar M, Gibson TJ, et al. : Degrons in cancer. PubMed DOI

Milles S, Salvi N, Blackledge M, et al. : Characterization of intrinsically disordered proteins and their dynamic complexes: From PubMed DOI

Mir S, Alhroub Y, Anyango S, et al. : PDBe: towards reusable data delivery infrastructure at protein data bank in Europe. PubMed DOI PMC

Mitrea DM, Kriwacki RW: Phase separation in biology; functional organization of a higher order. PubMed DOI PMC

Mottin L, Pasche E, Gobeill J, et al. : Triage by ranking to support the curation of protein interaction. PubMed DOI PMC

Mottin L, Pasche E, Gobeill J, et al. : Triage by ranking to support the curation of protein interactions. PubMed DOI PMC

Necci M, Piovesan D, Dosztányi Z, et al. : MobiDB-lite: fast and highly specific consensus prediction of intrinsic disorder in proteins. PubMed DOI

Neduva V, Russell RB: DILIMOT: discovery of linear motifs in proteins. PubMed DOI PMC

Nguyen HQ, Baxter BC, Brower K, et al. : Programmable Microfluidic Synthesis of Over One Thousand Uniquely Identifiable Spectral Codes. PubMed DOI PMC

Nielsen JT, Mulder FAA: There is Diversity in Disorder-"In all Chaos there is a Cosmos, in all Disorder a Secret Order". PubMed DOI PMC

Nodet G, Salmon L, Ozenne V, et al. : Quantitative description of backbone conformational sampling of unfolded proteins at amino acid resolution from NMR residual dipolar couplings. PubMed DOI

Oates ME, Romero P, Ishida T, et al. : D PubMed DOI PMC

Olsen JG, Teilum K, Kragelund BB: Behaviour of intrinsically disordered proteins in protein-protein complexes with an emphasis on fuzziness. PubMed DOI PMC

Orchard S, Ammari M, Aranda B, et al. : The MIntAct project--IntAct as a common curation platform for 11 molecular interaction databases. PubMed DOI PMC

Orchard S, Kerrien S, Abbani S, et al. : Protein interaction data curation: the International Molecular Exchange (IMEx) consortium. PubMed DOI PMC

Ozenne V, Bauer F, Salmon L, et al. : PubMed DOI

Pancsa R, Tompa P: Structural disorder in eukaryotes. PubMed DOI PMC

Peng Y, Cao S, Kiselar J, et al. : A Metastable Contact and Structural Disorder in the Estrogen Receptor Transactivation Domain. PubMed DOI PMC

Piovesan D, Tabaro F, Mičetić I, et al. : DisProt 7.0: a major update of the database of disordered proteins. PubMed DOI PMC

Piovesan D, Tabaro F, Paladin L, et al. : MobiDB 3.0: more annotations for intrinsic disorder, conformational diversity and interactions in proteins. PubMed DOI PMC

Plitzko JM, Schuler B, Selenko P: Structural Biology outside the box-inside the cell. PubMed DOI

Prilusky J, Felder CE, Zeev-Ben-Mordehai T, et al. : FoldIndex©: a simple tool to predict whether a given protein sequence is intrinsically unfolded. PubMed DOI

Raveh B, London N, Zimmerman L, et al. : Rosetta FlexPepDock PubMed DOI PMC

Santofimia-Castaño P, Xia Y, Lan W, et al. : Ligand-based design identifies a potent NUPR1 inhibitor exerting anticancer activity via necroptosis. PubMed DOI PMC

Schad E, Fichó E, Pancsa R, et al. : DIBS: a repository of disordered binding sites mediating interactions with ordered proteins. PubMed DOI PMC

Schuler B, Soranno A, Hofmann H, et al. : Single-Molecule FRET Spectroscopy and the Polymer Physics of Unfolded and Intrinsically Disordered Proteins. PubMed DOI

Scott JD, Pawson T: Cell signaling in space and time: where proteins come together and when they’re apart. PubMed DOI PMC

Shigemitsu Y, Hiroaki H: Common molecular pathogenesis of disease-related intrinsically disordered proteins revealed by NMR analysis. PubMed DOI

Shoemaker BA, Portman JJ, Wolynes PG: Speeding molecular recognition by using the folding funnel: the fly-casting mechanism. PubMed DOI PMC

Sickmeier M, Hamilton JA, LeGall T, et al. : DisProt: the Database of Disordered Proteins. PubMed DOI PMC

Sivade Dumousseau M, Alonso-López D, Ammari M, et al. : Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions. PubMed DOI PMC

Stanley N, Esteban-Martín S, De Fabritiis G: Progress in studying intrinsically disordered proteins with atomistic simulations. PubMed DOI

Tamiola K, Mulder FA: Using NMR chemical shifts to calculate the propensity for structural order and disorder in proteins. PubMed DOI

Tolchard J, Walpole SJ, Miles AJ, et al. : The intrinsically disordered Tarp protein from chlamydia binds actin with a partially preformed helix. PubMed DOI PMC

Tompa P: The interplay between structure and function in intrinsically unstructured proteins. PubMed DOI

Tompa P: Unstructural biology coming of age. PubMed DOI

Tompa P, Davey NE, Gibson TJ, et al. : A million peptide motifs for the molecular biologist. PubMed DOI

Trabuco LG, Lise S, Petsalaki E, et al. : PepSite: prediction of peptide-binding sites from protein surfaces. PubMed DOI PMC

Tribello GA, Bonomi M, Branduardi D, et al. : PLUMED2: New feathers for an old bird. DOI

Ulrich EL, Akutsu H, Doreleijers JF, et al. : BioMagResBank. PubMed DOI PMC

UniProt Consortium: UniProt: a worldwide hub of protein knowledge. PubMed DOI PMC

Uversky VN, Oldfield CJ, Dunker AK: Intrinsically disordered proteins in human diseases: introducing the D PubMed DOI

Valentini E, Kikhney AG, Previtali G, et al. : SASBDB, a repository for biological small-angle scattering data. PubMed DOI PMC

Vallat B, Webb B, Westbrook JD, et al. : Development of a Prototype System for Archiving Integrative/Hybrid Structure Models of Biological Macromolecules. PubMed DOI PMC

van der Lee R, Buljan M, Lang B, et al. : Classification of intrinsically disordered regions and proteins. PubMed DOI PMC

Van Roey K, Dinkel H, Weatheritt RJ, et al. : The switches.ELM resource: a compendium of conditional regulatory interaction interfaces. PubMed DOI

Van Roey K, Gibson TJ, Davey NE: Motif switches: decision-making in cell regulation. PubMed DOI

Van Roey K, Uyar B, Weatheritt RJ, et al. : Short linear motifs: ubiquitous and functionally diverse protein interaction modules directing cell regulation. PubMed DOI

Varadi M, Kosol S, Lebrun P, et al. : pE-DB: a database of structural ensembles of intrinsically disordered and of unfolded proteins. PubMed DOI PMC

Via A, Uyar B, Brun C, et al. : How pathogens use linear motifs to perturb host cell networks. PubMed DOI

Volkmer R: Synthesis and application of peptide arrays: quo vadis SPOT technology. PubMed DOI

Walsh I, Martin AJ, Di Domenico T, et al. : ESpritz: accurate and fast prediction of protein disorder. PubMed DOI

Weatheritt RJ, Davey NE, Gibson TJ: Linear motifs confer functional diversity onto splice variants. PubMed DOI PMC

Weatheritt RJ, Gibson TJ: Linear motifs: lost in (pre)translation. PubMed DOI

Whitmore L, Miles AJ, Mavridis L, et al. : PCDDB: new developments at the Protein Circular Dichroism Data Bank. PubMed DOI PMC

Wilkinson MD, Dumontier M, Aalbersberg IJ, et al. : The FAIR Guiding Principles for scientific data management and stewardship. PubMed DOI PMC

Wright PE, Dyson HJ: Intrinsically disordered proteins in cellular signalling and regulation. PubMed DOI PMC

Xue B, Dunker AK, Uversky VN: Orderly order in protein intrinsic disorder distribution: disorder in 3500 proteomes from viruses and the three domains of life. PubMed DOI

Xue B, Mizianty MJ, Kurgan L, et al. : Protein intrinsic disorder as a flexible armor and a weapon of HIV-1. PubMed DOI PMC

Yu C, Niu X, Jin F, et al. : Structure-based Inhibitor Design for the Intrinsically Disordered Protein c-Myc. PubMed DOI PMC

Nejnovějších 20 citací...

Zobrazit více v
Medvik | PubMed

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

. 2022 Jan 07 ; 50 (D1) : D480-D487.

Najít záznam

Citační ukazatele

Pouze přihlášení uživatelé

Možnosti archivace

Nahrávání dat ...