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PED in 2021 : A major update of the protein ensemble database for intrinsically disordered proteins

Lazar, Tamas (author)
Flanders Interuniversity Institute for Biotechnology,Vrije Universiteit Brussel (VUB)
Martínez-Pérez, Elizabeth (author)
European Molecular Biology Laboratory Heidelberg,Fundación Instituto Leloir
Quaglia, Federica (author)
University of Padova
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Hatos, András (author)
University of Padova
Chemes, Lucía B. (author)
National University of General San Martín
Iserte, Javier A. (author)
Fundación Instituto Leloir
Méndez, Nicolás A. (author)
National University of General San Martín
Garrone, Nicolás A. (author)
National University of General San Martín
Saldaño, Tadeo E. (author)
Quilmes National University
Marchetti, Julia (author)
Quilmes National University
Rueda, Ana Julia Velez (author)
Quilmes National University
Bernadó, Pau (author)
University of Montpellier
Blackledge, Martin (author)
University Grenoble Alpes
Cordeiro, Tiago N. (author)
University of Montpellier,NOVA University Lisbon
Fagerberg, Eric (author)
Lund University,Lunds universitet,Beräkningskemi,Enheten för fysikalisk och teoretisk kemi,Kemiska institutionen,Institutioner vid LTH,Lunds Tekniska Högskola,Computational Chemistry,Physical and theoretical chemistry,Department of Chemistry,Departments at LTH,Faculty of Engineering, LTH
Forman-Kay, Julie D. (author)
University of Toronto,Hospital for Sick Children, Toronto
Fornasari, Maria S. (author)
Quilmes National University
Gibson, Toby J. (author)
European Molecular Biology Laboratory Heidelberg
Gomes, Gregory Neal W. (author)
University of Toronto
Gradinaru, Claudiu C. (author)
University of Toronto
Head-Gordon, Teresa (author)
University of California, Berkeley
Jensen, Malene Ringkjøbing (author)
University Grenoble Alpes
Lemke, Edward A. (author)
Johannes-Gutenberg University Mainz
Longhi, Sonia (author)
Aix-Marseille University
Marino-Buslje, Cristina (author)
Fundación Instituto Leloir
Minervini, Giovanni (author)
University of Padova
Mittag, Tanja (author)
St Jude Children´s Research Hospital, Memphis
Monzon, Alexander Miguel (author)
University of Padova
Pappu, Rohit V. (author)
Washington University in St. Louis
Parisi, Gustavo (author)
Quilmes National University
Ricard-Blum, Sylvie (author)
Institute for Molecular and Supramolecular Chemistry and Biochemistry (ICBMS)
Ruff, Kiersten M. (author)
Washington University in St. Louis
Salladini, Edoardo (author)
Architecture et Fonction des Macromolécules Biologiques (AFMB)
Skepö, Marie (author)
Lund University,Lunds universitet,Beräkningskemi,Enheten för fysikalisk och teoretisk kemi,Kemiska institutionen,Institutioner vid LTH,Lunds Tekniska Högskola,LINXS - Institute of advanced Neutron and X-ray Science,Computational Chemistry,Physical and theoretical chemistry,Department of Chemistry,Departments at LTH,Faculty of Engineering, LTH,Faculty of Engineering, LTH
Svergun, Dmitri (author)
European Molecular Biology Laboratory Hamburg
Vallet, Sylvain D. (author)
Institute for Molecular and Supramolecular Chemistry and Biochemistry (ICBMS)
Varadi, Mihaly (author)
European Bioinformatics Institute
Tompa, Peter (author)
Research Centre for Natural Sciences of the Hungarian Academy of Sciences,Vrije Universiteit Brussel (VUB),Flanders Interuniversity Institute for Biotechnology
Tosatto, Silvio C.E. (author)
University of Padova
Piovesan, Damiano (author)
University of Padova
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 (creator_code:org_t)
2020-12-10
2021
English 8 s.
In: Nucleic Acids Research. - : Oxford University Press (OUP). - 0305-1048 .- 1362-4962. ; 49:D1, s. 404-411
  • Journal article (peer-reviewed)
Abstract Subject headings
Close  
  • The Protein Ensemble Database (PED) (https://proteinensemble.org), which holds structural ensembles of intrinsically disordered proteins (IDPs), has been significantly updated and upgraded since its last release in 2016. The new version, PED 4.0, has been completely redesigned and reimplemented with cutting-edge technology and now holds about six times more data (162 versus 24 entries and 242 versus 60 structural ensembles) and a broader representation of state of the art ensemble generation methods than the previous version. The database has a completely renewed graphical interface with an interactive feature viewer for region-based annotations, and provides a series of descriptors of the qualitative and quantitative properties of the ensembles. High quality of the data is guaranteed by a new submission process, which combines both automatic and manual evaluation steps. A team of biocurators integrate structured metadata describing the ensemble generation methodology, experimental constraints and conditions. A new search engine allows the user to build advanced queries and search all entry fields including cross-references to IDP-related resources such as DisProt, MobiDB, BMRB and SASBDB. We expect that the renewed PED will be useful for researchers interested in the atomic-level understanding of IDP function, and promote the rational, structure-based design of IDP-targeting drugs.

Subject headings

NATURVETENSKAP  -- Kemi -- Teoretisk kemi (hsv//swe)
NATURAL SCIENCES  -- Chemical Sciences -- Theoretical Chemistry (hsv//eng)

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art (subject category)
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