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PED in 2021 : A maj...
PED in 2021 : A major update of the protein ensemble database for intrinsically disordered proteins
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- Lazar, Tamas (author)
- Vrije Universiteit Brussel (VUB),Flanders Interuniversity Institute for Biotechnology
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- Martínez-Pérez, Elizabeth (author)
- European Molecular Biology Laboratory Heidelberg,Fundación Instituto Leloir
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- Quaglia, Federica (author)
- University of Padova
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- Hatos, András (author)
- University of Padova
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- Chemes, Lucía B. (author)
- National University of General San Martín
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- Iserte, Javier A. (author)
- Fundación Instituto Leloir
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- Méndez, Nicolás A. (author)
- National University of General San Martín
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- Garrone, Nicolás A. (author)
- National University of General San Martín
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- Saldaño, Tadeo E. (author)
- Quilmes National University
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- Marchetti, Julia (author)
- Quilmes National University
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- Rueda, Ana Julia Velez (author)
- Quilmes National University
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- Bernadó, Pau (author)
- University of Montpellier
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- Blackledge, Martin (author)
- University Grenoble Alpes
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- Cordeiro, Tiago N. (author)
- NOVA University Lisbon,University of Montpellier
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- 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
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- Forman-Kay, Julie D. (author)
- University of Toronto,Hospital for Sick Children, Toronto
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- Fornasari, Maria S. (author)
- Quilmes National University
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- Gibson, Toby J. (author)
- European Molecular Biology Laboratory Heidelberg
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- Gomes, Gregory Neal W. (author)
- University of Toronto
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- Gradinaru, Claudiu C. (author)
- University of Toronto
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- Head-Gordon, Teresa (author)
- University of California, Berkeley
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- Jensen, Malene Ringkjøbing (author)
- University Grenoble Alpes
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- Lemke, Edward A. (author)
- Johannes-Gutenberg University Mainz
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- Longhi, Sonia (author)
- Aix-Marseille University
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- Marino-Buslje, Cristina (author)
- Fundación Instituto Leloir
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- Minervini, Giovanni (author)
- University of Padova
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- Mittag, Tanja (author)
- St Jude Children´s Research Hospital, Memphis
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- Monzon, Alexander Miguel (author)
- University of Padova
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- Pappu, Rohit V. (author)
- Washington University in St. Louis
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- Parisi, Gustavo (author)
- Quilmes National University
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- Ricard-Blum, Sylvie (author)
- Institute for Molecular and Supramolecular Chemistry and Biochemistry (ICBMS)
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- Ruff, Kiersten M. (author)
- Washington University in St. Louis
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- Salladini, Edoardo (author)
- Architecture et Fonction des Macromolécules Biologiques (AFMB)
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- 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
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- Svergun, Dmitri (author)
- European Molecular Biology Laboratory Hamburg
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- Vallet, Sylvain D. (author)
- Institute for Molecular and Supramolecular Chemistry and Biochemistry (ICBMS)
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- Varadi, Mihaly (author)
- European Bioinformatics Institute
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- Tompa, Peter (author)
- Flanders Interuniversity Institute for Biotechnology,Research Centre for Natural Sciences of the Hungarian Academy of Sciences,Vrije Universiteit Brussel (VUB)
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- Tosatto, Silvio C.E. (author)
- University of Padova
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- Piovesan, Damiano (author)
- University of Padova
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(creator_code:org_t)
- 2020-12-10
- 2021
- English 8 s.
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In: Nucleic Acids Research. - : Oxford University Press (OUP). - 0305-1048 .- 1362-4962. ; 49:D1, s. 404-411
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http://dx.doi.org/10... (free)
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https://doi.org/10.1...
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Abstract
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- 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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Lazar, Tamas
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Martínez-Pérez, ...
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Quaglia, Federic ...
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Hatos, András
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Chemes, Lucía B.
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Iserte, Javier A ...
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Méndez, Nicolás ...
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Garrone, Nicolás ...
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Saldaño, Tadeo E ...
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Marchetti, Julia
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Rueda, Ana Julia ...
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Bernadó, Pau
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Blackledge, Mart ...
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Cordeiro, Tiago ...
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Fagerberg, Eric
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Forman-Kay, Juli ...
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Fornasari, Maria ...
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Gibson, Toby J.
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Gomes, Gregory N ...
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Gradinaru, Claud ...
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Head-Gordon, Ter ...
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Jensen, Malene R ...
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Lemke, Edward A.
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Longhi, Sonia
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Marino-Buslje, C ...
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Minervini, Giova ...
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Mittag, Tanja
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Monzon, Alexande ...
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Pappu, Rohit V.
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Parisi, Gustavo
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Ricard-Blum, Syl ...
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Ruff, Kiersten M ...
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Salladini, Edoar ...
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Skepö, Marie
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Svergun, Dmitri
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Vallet, Sylvain ...
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Varadi, Mihaly
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Tompa, Peter
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Tosatto, Silvio ...
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Piovesan, Damian ...
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- NATURAL SCIENCES
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Nucleic Acids Re ...
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Lund University