PED in 2021: a major update of the protein ensemble database for intrinsically disordered proteins,Nucleic Acids Research

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PED in 2021: a major update of the protein ensemble database for intrinsically disordered proteins
Nucleic Acids Research ( IF 16.6 ) Pub Date : 2020-12-10 , DOI: 10.1093/nar/gkaa1021
Tamas Lazar _{1,

2} , Elizabeth Martínez-Pérez _{3,

4} , Federica Quaglia ₅ , András Hatos ₅ , Lucía B Chemes ₆ , Javier A Iserte ₃ , Nicolás A Méndez ₆ , Nicolás A Garrone ₆ , Tadeo E Saldaño ₇ , Julia Marchetti ₇ , Ana Julia Velez Rueda ₇ , Pau Bernadó ₈ , Martin Blackledge ₉ , Tiago N Cordeiro _{8,

10} , Eric Fagerberg ₁₁ , Julie D Forman-Kay _{12,

13} , Maria S Fornasari ₇ , Toby J Gibson ₄ , Gregory-Neal W Gomes _{14,

15} , Claudiu C Gradinaru _{14,

15} , Teresa Head-Gordon ₁₆ , Malene Ringkjøbing Jensen ₉ , Edward A Lemke _{17,

18} , Sonia Longhi ₁₉ , Cristina Marino-Buslje ₃ , Giovanni Minervini ₅ , Tanja Mittag ₂₀ , Alexander Miguel Monzon ₅ , Rohit V Pappu ₂₁ , Gustavo Parisi ₇ , Sylvie Ricard-Blum ₂₂ , Kiersten M Ruff ₂₁ , Edoardo Salladini ₁₉ , Marie Skepö _{11,

23} , Dmitri Svergun ₂₄ , Sylvain D Vallet ₂₂ , Mihaly Varadi ₂₅ , Peter Tompa _{1,

2,

26} , Silvio C E Tosatto ₅ , Damiano Piovesan ₅

Affiliation

VIB-VUB Center for Structural Biology, Flanders Institute for Biotechnology, Brussels 1050, Belgium.
Structural Biology Brussels, Bioengineering Sciences Department, Vrije Universiteit Brussel, Brussels 1050, Belgium.
Bioinformatics Unit, Fundación Instituto Leloir, Buenos Aires, C1405BWE, Argentina.
Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany.
Dept. of Biomedical Sciences, University of Padua, Padova 35131, Italy.
Instituto de Investigaciones Biotecnológicas "Dr. Rodolfo A. Ugalde'', IIB-UNSAM, IIBIO-CONICET, Universidad Nacional de SanMartín, CP1650 San Martín, Buenos Aires, Argentina.
Laboratorio de Química y Biología Computacional, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal B1876BXD, Buenos Aires, Argentina.
Centre de Biochimie Structurale (CBS), CNRS, INSERM, University of Montpellier, Montpellier 34090, France.
Univ. Grenoble Alpes, CNRS, CEA, IBS, Grenoble, F-38000, France.
Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras 2780-157, Portugal.
Theoretical Chemistry, Lund University, Lund, POB 124, SE-221 00, Sweden.
Molecular Medicine Program, Hospital for Sick Children, Toronto, M5G 1X8, Ontario, Canada.
Department of Biochemistry, University of Toronto, Toronto, M5S 1A8, Ontario, Canada.
Department of Physics, University of Toronto, Toronto, M5S 1A7, Ontario, Canada.
Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, L5L 1C6, Ontario, Canada.
Departments of Chemistry, Bioengineering, Chemical and Biomolecular Engineering University of California, Berkeley, CA 94720, USA.
Biocentre, Johannes Gutenberg-University Mainz, Mainz 55128, Germany.
Institute of Molecular Biology, Mainz 55128, Germany.
Aix-Marseille University, CNRS, Architecture et Fonction des Macromolécules Biologiques (AFMB), Marseille 13288, France.
Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
Department of Biomedical Engineering, Center for Science & Engineering of Living Systems (CSELS), Washington University in St. Louis, MO 63130, USA.
Univ Lyon, University Claude Bernard Lyon 1, CNRS, INSA Lyon, CPE, Institute of Molecular and Supramolecular Chemistry and Biochemistry (ICBMS), UMR 5246, Villeurbanne, 69629 Lyon Cedex 07, France.
LINXS - Lund Institute of Advanced Neutron and X-ray Science, Lund 223 70, Sweden.
European Molecular Biology Laboratory, Hamburg Unit, Hamburg 22607, Germany.
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, CB10 1SD, UK.
Institute of Enzymology, Research Centre for Natural Sciences, Budapest, 1117, Hungary.

Abstract

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.

中文翻译：

2021 年的 PED：本质上无序蛋白质的蛋白质集合数据库的重大更新

摘要

蛋白质集合数据库 (PED) (https://proteinensemble.org) 包含固有无序蛋白质 (IDP) 的结构集合，自 2016 年上次发布以来已进行了重大更新和升级。新版本 PED 4.0完全重新设计并使用尖端技术重新实现，现在拥有约 6 倍的数据（162 对 24 条目和 242 对 60 结构集成）和更广泛的代表最先进的集成生成方法比以前的版本。该数据库具有完全更新的图形界面，带有用于基于区域的注释的交互式特征查看器，并提供了一系列关于集合的定性和定量属性的描述符。新的提交流程保证了数据的高质量，它结合了自动和手动评估步骤。一个生物策展人团队整合了描述集合生成方法、实验约束和条件的结构化元数据。新的搜索引擎允许用户构建高级查询并搜索所有条目字段，包括对 IDP 相关资源（如 DisProt、MobiDB、BMRB 和 SASBDB）的交叉引用。我们希望更新的 PED 将有助于对 IDP 功能的原子级理解感兴趣的研究人员，并促进 IDP 靶向药物的合理、基于结构的设计。新的搜索引擎允许用户构建高级查询并搜索所有条目字段，包括对 IDP 相关资源（如 DisProt、MobiDB、BMRB 和 SASBDB）的交叉引用。我们希望更新的 PED 将有助于对 IDP 功能的原子级理解感兴趣的研究人员，并促进 IDP 靶向药物的合理、基于结构的设计。新的搜索引擎允许用户构建高级查询并搜索所有条目字段，包括对 IDP 相关资源（如 DisProt、MobiDB、BMRB 和 SASBDB）的交叉引用。我们希望更新的 PED 将有助于对 IDP 功能的原子级理解感兴趣的研究人员，并促进 IDP 靶向药物的合理、基于结构的设计。

更新日期：2021-01-03

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