Literature DB >> 33237286

UniProt: the universal protein knowledgebase in 2021.

.   

Abstract

The aim of the UniProt Knowledgebase is to provide users with a comprehensive, high-quality and freely accessible set of protein sequences annotated with functional information. In this article, we describe significant updates that we have made over the last two years to the resource. The number of sequences in UniProtKB has risen to approximately 190 million, despite continued work to reduce sequence redundancy at the proteome level. We have adopted new methods of assessing proteome completeness and quality. We continue to extract detailed annotations from the literature to add to reviewed entries and supplement these in unreviewed entries with annotations provided by automated systems such as the newly implemented Association-Rule-Based Annotator (ARBA). We have developed a credit-based publication submission interface to allow the community to contribute publications and annotations to UniProt entries. We describe how UniProtKB responded to the COVID-19 pandemic through expert curation of relevant entries that were rapidly made available to the research community through a dedicated portal. UniProt resources are available under a CC-BY (4.0) license via the web at https://www.uniprot.org/.
© The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.

Entities:  

Mesh:

Substances:

Year:  2021        PMID: 33237286      PMCID: PMC7778908          DOI: 10.1093/nar/gkaa1100

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN: 0305-1048            Impact factor:   16.971


  45 in total

1.  ClinGen Pathogenicity Calculator: a configurable system for assessing pathogenicity of genetic variants.

Authors:  Ronak Y Patel; Neethu Shah; Andrew R Jackson; Rajarshi Ghosh; Piotr Pawliczek; Sameer Paithankar; Aaron Baker; Kevin Riehle; Hailin Chen; Sofia Milosavljevic; Chris Bizon; Shawn Rynearson; Tristan Nelson; Gail P Jarvik; Heidi L Rehm; Steven M Harrison; Danielle Azzariti; Bradford Powell; Larry Babb; Sharon E Plon; Aleksandar Milosavljevic
Journal:  Genome Med       Date:  2017-01-12       Impact factor: 11.117

2.  The international nucleotide sequence database collaboration.

Authors:  Ilene Karsch-Mizrachi; Toshihisa Takagi; Guy Cochrane
Journal:  Nucleic Acids Res       Date:  2018-01-04       Impact factor: 16.971

3.  The Proteins API: accessing key integrated protein and genome information.

Authors:  Andrew Nightingale; Ricardo Antunes; Emanuele Alpi; Borisas Bursteinas; Leonardo Gonzales; Wudong Liu; Jie Luo; Guoying Qi; Edd Turner; Maria Martin
Journal:  Nucleic Acids Res       Date:  2017-07-03       Impact factor: 16.971

4.  ProtVista: visualization of protein sequence annotations.

Authors:  Xavier Watkins; Leyla J Garcia; Sangya Pundir; Maria J Martin
Journal:  Bioinformatics       Date:  2017-07-01       Impact factor: 6.937

5.  Enzyme annotation in UniProtKB using Rhea.

Authors:  Anne Morgat; Thierry Lombardot; Elisabeth Coudert; Kristian Axelsen; Teresa Batista Neto; Sebastien Gehant; Parit Bansal; Jerven Bolleman; Elisabeth Gasteiger; Edouard de Castro; Delphine Baratin; Monica Pozzato; Ioannis Xenarios; Sylvain Poux; Nicole Redaschi; Alan Bridge
Journal:  Bioinformatics       Date:  2020-03-01       Impact factor: 6.937

6.  InterPro in 2019: improving coverage, classification and access to protein sequence annotations.

Authors:  Alex L Mitchell; Teresa K Attwood; Patricia C Babbitt; Matthias Blum; Peer Bork; Alan Bridge; Shoshana D Brown; Hsin-Yu Chang; Sara El-Gebali; Matthew I Fraser; Julian Gough; David R Haft; Hongzhan Huang; Ivica Letunic; Rodrigo Lopez; Aurélien Luciani; Fabio Madeira; Aron Marchler-Bauer; Huaiyu Mi; Darren A Natale; Marco Necci; Gift Nuka; Christine Orengo; Arun P Pandurangan; Typhaine Paysan-Lafosse; Sebastien Pesseat; Simon C Potter; Matloob A Qureshi; Neil D Rawlings; Nicole Redaschi; Lorna J Richardson; Catherine Rivoire; Gustavo A Salazar; Amaia Sangrador-Vegas; Christian J A Sigrist; Ian Sillitoe; Granger G Sutton; Narmada Thanki; Paul D Thomas; Silvio C E Tosatto; Siew-Yit Yong; Robert D Finn
Journal:  Nucleic Acids Res       Date:  2019-01-08       Impact factor: 16.971

7.  Community curation in PomBase: enabling fission yeast experts to provide detailed, standardized, sharable annotation from research publications.

Authors:  Antonia Lock; Midori A Harris; Kim Rutherford; Jacqueline Hayles; Valerie Wood
Journal:  Database (Oxford)       Date:  2020-01-01       Impact factor: 3.451

8.  The DisGeNET knowledge platform for disease genomics: 2019 update.

Authors:  Janet Piñero; Juan Manuel Ramírez-Anguita; Josep Saüch-Pitarch; Francesco Ronzano; Emilio Centeno; Ferran Sanz; Laura I Furlong
Journal:  Nucleic Acids Res       Date:  2020-01-08       Impact factor: 16.971

9.  The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences.

Authors:  Rachel Drysdale; Charles E Cook; Robert Petryszak; Vivienne Baillie-Gerritsen; Mary Barlow; Elisabeth Gasteiger; Franziska Gruhl; Jürgen Haas; Jerry Lanfear; Rodrigo Lopez; Nicole Redaschi; Heinz Stockinger; Daniel Teixeira; Aravind Venkatesan; Niklas Blomberg; Christine Durinx; Johanna McEntyre
Journal:  Bioinformatics       Date:  2020-04-15       Impact factor: 6.937

10.  The jPOST environment: an integrated proteomics data repository and database.

Authors:  Yuki Moriya; Shin Kawano; Shujiro Okuda; Yu Watanabe; Masaki Matsumoto; Tomoyo Takami; Daiki Kobayashi; Yoshinori Yamanouchi; Norie Araki; Akiyasu C Yoshizawa; Tsuyoshi Tabata; Mio Iwasaki; Naoyuki Sugiyama; Satoshi Tanaka; Susumu Goto; Yasushi Ishihama
Journal:  Nucleic Acids Res       Date:  2019-01-08       Impact factor: 16.971

View more
  1001 in total

1.  LitSuggest: a web-based system for literature recommendation and curation using machine learning.

Authors:  Alexis Allot; Kyubum Lee; Qingyu Chen; Ling Luo; Zhiyong Lu
Journal:  Nucleic Acids Res       Date:  2021-07-02       Impact factor: 16.971

2.  Crystal structure and functional properties of the human CCR4-CAF1 deadenylase complex.

Authors:  Ying Chen; Elena Khazina; Elisa Izaurralde; Oliver Weichenrieder
Journal:  Nucleic Acids Res       Date:  2021-06-21       Impact factor: 16.971

3.  In vivo and in vitro human gene essentiality estimations capture contrasting functional constraints.

Authors:  Jose Luis Caldu-Primo; Jorge Armando Verduzco-Martínez; Elena R Alvarez-Buylla; Jose Davila-Velderrain
Journal:  NAR Genom Bioinform       Date:  2021-07-13

Review 4.  Vascular Endothelial Galectins in Leukocyte Trafficking.

Authors:  Abbey Lightfoot; Helen M McGettrick; Asif J Iqbal
Journal:  Front Immunol       Date:  2021-06-01       Impact factor: 7.561

5.  The adverse metabolic effects of branched-chain amino acids are mediated by isoleucine and valine.

Authors:  Deyang Yu; Nicole E Richardson; Cara L Green; Alexandra B Spicer; Michaela E Murphy; Victoria Flores; Cholsoon Jang; Ildiko Kasza; Maria Nikodemova; Matthew H Wakai; Jay L Tomasiewicz; Shany E Yang; Blake R Miller; Heidi H Pak; Jacqueline A Brinkman; Jennifer M Rojas; William J Quinn; Eunhae P Cheng; Elizabeth N Konon; Lexington R Haider; Megan Finke; Michelle Sonsalla; Caroline M Alexander; Joshua D Rabinowitz; Joseph A Baur; Kristen C Malecki; Dudley W Lamming
Journal:  Cell Metab       Date:  2021-04-21       Impact factor: 27.287

6.  A Human Endogenous Bornavirus-Like Nucleoprotein Encodes a Mitochondrial Protein Associated with Cell Viability.

Authors:  Kan Fujino; Masayuki Horie; Shohei Kojima; Sae Shimizu; Aya Nabekura; Hiroko Kobayashi; Akiko Makino; Tomoyuki Honda; Keizo Tomonaga
Journal:  J Virol       Date:  2021-06-24       Impact factor: 5.103

7.  The Protein Interactome of Glycolysis in Escherichia coli.

Authors:  Shomeek Chowdhury; Stephen Hepper; Mudassir K Lodi; Milton H Saier; Peter Uetz
Journal:  Proteomes       Date:  2021-04-06

8.  Proteomic Identification of Bombyx mori Organelles Using the Engineered Ascorbate Peroxidase APEX and Development of Silkworm Organelle Proteome Database (SilkOrganPDB).

Authors:  Tian Li; Chen Xu; Jinzhi Xu; Jian Luo; Bin Yu; Xianzhi Meng; Chunfeng Li; Guoqing Pan; Zeyang Zhou
Journal:  Int J Mol Sci       Date:  2021-05-10       Impact factor: 5.923

Review 9.  DNA Damage Response in the Adaptive Arm of the Immune System: Implications for Autoimmunity.

Authors:  Theodora Manolakou; Panayotis Verginis; Dimitrios T Boumpas
Journal:  Int J Mol Sci       Date:  2021-05-29       Impact factor: 5.923

Review 10.  Oncogenic Potential of the Dual-Function Protein MEX3A.

Authors:  Marcell Lederer; Simon Müller; Markus Glaß; Nadine Bley; Christian Ihling; Andrea Sinz; Stefan Hüttelmaier
Journal:  Biology (Basel)       Date:  2021-05-07
View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.