Einzeltreffer — DigiBib

The archiving and dissemination of protein and nucleic acid structures as well as their structural, functional and biophysical annotations is an essential task that enables the broader scientific community to conduct impactful research in multiple fields of the life sciences. The Protein Data Bank in Europe (PDBe; pdbe.org) team develops and maintains several databases and web services to address this fundamental need. From data archiving as a member of the Worldwide PDB consortium (wwPDB; wwpdb.org), to the PDBe Knowledge Base (PDBe-KB; pdbekb.org), we provide data, data-access mechanisms, and visualizations that facilitate basic and applied research and education across the life sciences. Here, we provide an overview of the structural data and annotations that we integrate and make freely available. We describe the web services and data visualization tools we offer, and provide information on how to effectively use or even further develop them. Finally, we discuss the direction of our data services, and how we aim to tackle new challenges that arise from the recent, unprecedented advances in the field of structure determination and protein structure modeling.

Titel:	PDBe and PDBe-KB: Providing high-quality, up-to-date and integrated resources of macromolecular structures to support basic and applied research and education.
Autor/in / Beteiligte Person:	Varadi, M ; Anyango, S ; Appasamy, SD ; Armstrong, D ; Bage, M ; Berrisford, J ; Choudhary, P ; Bertoni, D ; Deshpande, M ; Leines, GD ; Ellaway, J ; Evans, G ; Gaborova, R ; Gupta, D ; Gutmanas, A ; Harrus, D ; Kleywegt, GJ ; Bueno, WM ; Nadzirin, N ; Nair, S ; Pravda, L ; Afonso, MQL ; Sehnal, D ; Tanweer, A ; Tolchard, J ; Abrams, C ; Dunlop, R ; Velankar, S
Link:	Full Text Finder (Volltext)
Zeitschrift:	Protein science : a publication of the Protein Society, Jg. 31 (2022-10-01), Heft 10, S. e4439
Veröffentlichung:	2001- : Woodbury, NY : Cold Spring Harbor Laboratory Press ; <i>Original Publication</i>: New York, N.Y. : Cambridge University Press, c1992-, 2022
Medientyp:	academicJournal
ISSN:	1469-896X (electronic)
DOI:	10.1002/pro.4439
Schlagwort:	Databases, Protein Europe Protein Conformation Nucleic Acids Proteins chemistry
Sonstiges:	Nachgewiesen in: MEDLINE Sprachen: English Publication Type: Journal Article; Research Support, Non-U.S. Gov't Language: English [Protein Sci] 2022 Oct; Vol. 31 (10), pp. e4439. MeSH Terms: Nucleic Acids* ; Proteins* / chemistry ; Databases, Protein ; Europe ; Protein Conformation References: Nucleic Acids Res. 2010 Jul;38(Web Server issue):W469-73. (PMID: 20513649) ; Bioinformatics. 2019 Oct 15;35(20):4168-4169. (PMID: 30874800) ; Nucleic Acids Res. 2022 Jan 7;50(D1):D534-D542. (PMID: 34755867) ; Sci Data. 2016 Mar 15;3:160018. (PMID: 26978244) ; Nucleic Acids Res. 2020 Jan 8;48(D1):D335-D343. (PMID: 31691821) ; Protein Sci. 2018 Jan;27(1):129-134. (PMID: 28875543) ; Nucleic Acids Res. 2018 Jan 4;46(D1):D399-D405. (PMID: 29036719) ; Methods Mol Biol. 2020;2112:187-218. (PMID: 32006287) ; Rev Immunogenet. 2000;2(4):461-7. (PMID: 12361089) ; Nucleic Acids Res. 2019 Jan 8;47(D1):D520-D528. (PMID: 30357364) ; J Mol Biol. 2021 May 28;433(11):166704. (PMID: 33186584) ; Nucleic Acids Res. 2020 Jan 8;48(D1):D344-D353. (PMID: 31584092) ; Curr Protoc Bioinformatics. 2016 Jun 20;54:1.30.1-1.30.33. (PMID: 27322403) ; Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W342-6. (PMID: 15980485) ; Science. 2022 Jun 10;376(6598):eabm9506. (PMID: 35679397) ; Science. 2021 Aug 20;373(6557):871-876. (PMID: 34282049) ; Nucleic Acids Res. 2021 Jan 8;49(D1):D1074-D1082. (PMID: 33219674) ; Vaccines (Basel). 2022 May 30;10(6):. (PMID: 35746483) ; Nucleic Acids Res. 2017 Jan 4;45(D1):D282-D288. (PMID: 27789697) ; Nat Struct Biol. 2000 Nov;7 Suppl:960-3. (PMID: 11104000) ; Nucleic Acids Res. 2021 Jan 8;49(D1):D344-D354. (PMID: 33156333) ; F1000Res. 2020 Apr 22;9:. (PMID: 32566135) ; Bioinformatics. 2021 Jun 03;:. (PMID: 34081107) ; J Mol Biol. 2022 Jan 30;434(2):167377. (PMID: 34838520) ; BMC Bioinformatics. 2014 Dec 30;15:427. (PMID: 25547242) ; Curr Opin Struct Biol. 2022 Jun;74:102372. (PMID: 35439658) ; Nature. 2021 Aug;596(7873):583-589. (PMID: 34265844) ; Nucleic Acids Res. 2022 Jan 7;50(D1):D439-D444. (PMID: 34791371) ; Front Pharmacol. 2022 Mar 18;13:843043. (PMID: 35370688) ; Bioinformatics. 2019 Sep 15;35(18):3510-3511. (PMID: 30759194) ; Nat Commun. 2021 Jun 9;12(1):3494. (PMID: 34108470) ; Nucleic Acids Res. 2014 Jul;42(Web Server issue):W264-70. (PMID: 24728994) ; Structure. 2017 Mar 7;25(3):536-545. (PMID: 28190782) ; Science. 2022 Jun 10;376(6598):eabm9326. (PMID: 35679401) ; Hum Genet. 2021 May;140(5):805-812. (PMID: 33502607) ; Nat Struct Mol Biol. 2022 Aug;29(8):813-819. (PMID: 35578024) ; Nucleic Acids Res. 2021 Jan 8;49(D1):D412-D419. (PMID: 33125078) ; Nucleic Acids Res. 2021 Jul 2;49(W1):W431-W437. (PMID: 33956157) ; Nucleic Acids Res. 2019 Jan 8;47(D1):D482-D489. (PMID: 30445541) ; Nucleic Acids Res. 2020 Jan 8;48(D1):D376-D382. (PMID: 31724711) ; Protein Sci. 2018 Jan;27(1):316-330. (PMID: 29067736) ; Nucleic Acids Res. 2019 Jan 8;47(D1):D280-D284. (PMID: 30398663) ; Nucleic Acids Res. 2021 Jan 8;49(D1):D480-D489. (PMID: 33237286) ; J Math Biol. 2008 Jan;56(1-2):215-52. (PMID: 17694311) ; Nucleic Acids Res. 2022 Jan 7;50(D1):D988-D995. (PMID: 34791404) ; PLoS Biol. 2022 May 16;20(5):e3001636. (PMID: 35576205) ; Curr Protoc Bioinformatics. 2018 Mar;61(1):5.10.1-5.10.12. (PMID: 30008982) Grant Information: BB/R015201/1 United Kingdom BB_ Biotechnology and Biological Sciences Research Council; 223739/Z/21/Z United Kingdom WT_ Wellcome Trust; BB/V004247/1 United Kingdom BB_ Biotechnology and Biological Sciences Research Council; BB/V016113/1 United Kingdom BB_ Biotechnology and Biological Sciences Research Council; BB/S017135/1 United Kingdom BB_ Biotechnology and Biological Sciences Research Council; 221327/Z/20/Z United Kingdom WT_ Wellcome Trust; BB/T01959X/1 United Kingdom BB_ Biotechnology and Biological Sciences Research Council; BB/P025846/1 United Kingdom BB_ Biotechnology and Biological Sciences Research Council; BB/M011674/1 United Kingdom BB_ Biotechnology and Biological Sciences Research Council; BB/P024351/1 United Kingdom BB_ Biotechnology and Biological Sciences Research Council; 104948/Z/14/Z United Kingdom WT_ Wellcome Trust; 218303/Z/19/Z United Kingdom WT_ Wellcome Trust; BB/W017970/1 United Kingdom BB_ Biotechnology and Biological Sciences Research Council; BB/V018779/1 United Kingdom BB_ Biotechnology and Biological Sciences Research Council; BB/S020071/1 United Kingdom BB_ Biotechnology and Biological Sciences Research Council; United Kingdom WT_ Wellcome Trust Contributed Indexing: Keywords: bioinformatics; databases; protein data bank; structural biology Substance Nomenclature: 0 (Nucleic Acids) ; 0 (Proteins) Entry Date(s): Date Created: 20220929 Date Completed: 20220930 Latest Revision: 20221026 Update Code: 20240513 PubMed Central ID: PMC9517934

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PDBe and PDBe-KB: Providing high-quality, up-to-date and integrated resources of macromolecular structures to support basic and applied research and education.