The UniProtKB/Swiss-Prot Tox-Prot program: A central hub of integrated venom protein data

被引:149
|
作者
Jungo, Florence [1 ]
Bougueleret, Lydie [1 ]
Xenarios, Ioannis [1 ,2 ]
Poux, Sylvain [1 ]
机构
[1] Ctr Med Univ Geneva, Swiss Inst Bioinformat, CH-1211 Geneva 4, Switzerland
[2] Swiss Inst Bioinformat, Vital IT Grp, CH-1015 Lausanne, Switzerland
基金
美国国家卫生研究院;
关键词
UniProtKB/Swiss-Prot Tox-Prot program; Database; Curation; Venom protein; Animal toxin; Bioinformatics; POSTTRANSLATIONAL MODIFICATIONS; NOMENCLATURE; ANNOTATION; EVOLUTION; COMPLEXITY; SEQUENCES; KNOWLEDGE; CDNA;
D O I
10.1016/j.toxicon.2012.03.010
中图分类号
R9 [药学];
学科分类号
1007 ;
摘要
Animal toxins are of interest to a wide range of scientists, due to their numerous applications in pharmacology, neurology, hematology, medicine, and drug research. This, and to a lesser extent the development of new performing tools in transcriptomics and proteomics, has led to an increase in toxin discovery. In this context, providing publicly available data on animal toxins has become essential. The UniProtKB/Swiss-Prot Tox-Prot program (http://www.uniprot.org/program/Toxins) plays a crucial role by providing such an access to venom protein sequences and functions from all venomous species. This program has up to now curated more than 5000 venom proteins to the high-quality standards of UniProtKB/Swiss-Prot (release 2012_02). Proteins targeted by these toxins are also available in the knowledgebase. This paper describes in details the type of information provided by UniProtKB/Swiss-Prot for toxins, as well as the structured format of the knowledgebase. (c) 2012 Elsevier Ltd. All rights reserved.
引用
收藏
页码:551 / 557
页数:7
相关论文
共 46 条
  • [1] Tox-Prot, the toxin protein annotation program of the Swiss-Prot protein knowledgebase
    Jungo, F
    Bairoch, A
    TOXICON, 2005, 45 (03) : 293 - 301
  • [2] UniProtKB/Swiss-Prot: the protein sequence knowledgebase
    Stutz, A.
    Bairoch, A.
    Estreicher, A.
    FEBS JOURNAL, 2006, 273 : 62 - 62
  • [3] The Plant Proteome Annotation Program (PPAP) of UniProtKB/Swiss-Prot
    Lieberherr, D
    Boutet, E
    Tognolli, M
    Schneider, M
    Bairoch, A
    FEBS JOURNAL, 2005, 272 : 110 - 110
  • [4] UNIPROTKB/SWISS-PROT and the human proteomics initiative
    Jimenez, S.
    Rojas, S. Ferro
    Bairoch, A.
    MOLECULAR & CELLULAR PROTEOMICS, 2005, 4 (08) : S23 - S23
  • [5] UniProtKB/Swiss-Prot: from sequences to functions
    Bairoch, A.
    FEBS JOURNAL, 2009, 276 : 9 - 9
  • [6] UniProtKB/Swiss-Prot: New and future developments
    Bairoch, Amos
    DATA INTEGRATION IN THE LIFE SCIENCES, PROCEEDINGS, 2008, 5109 : 204 - 206
  • [7] The UniProtKB/Swiss-Prot knowledgebase and its Plant Proteome Annotation Program
    Schneider, Michel
    Lane, Lydie
    Boutet, Emmanuel
    Lieberherr, Damien
    Tognolli, Michael
    Bougueleret, Lydie
    Baiyoch, Amos
    JOURNAL OF PROTEOMICS, 2009, 72 (03) : 567 - 573
  • [8] Mining the UniProtKB/Swiss-Prot database for antimicrobial peptides
    Li, Chenkai
    Sutherland, Darcy
    Salehi, Ali
    Richter, Amelia
    Lin, Diana
    Aninta, Sambina Islam
    Ebrahimikondori, Hossein
    Yanai, Anat
    Coombe, Lauren
    Warren, Rene L.
    Kotkoff, Monica
    Hoang, Linda M. N.
    Helbing, Caren C.
    Birol, Inanc
    PROTEIN SCIENCE, 2025, 34 (04)
  • [9] On expert curation and scalability: UniProtKB/Swiss-Prot as a case study
    Poux, Sylvain
    Arighi, Cecilia N.
    Magrane, Michele
    Bateman, Alex
    Wei, Chih-Hsuan
    Lu, Zhiyong
    Boutet, Emmanuel
    Bye-A-Jee, Hema
    Famiglietti, Maria Livia
    Roechert, Bernd
    Martin, Maria Jesus
    O'Donovan, Claire
    Alpi, Emanuele
    Antunes, Ricardo
    Bely, Benoit
    Bingley, Mark
    Bonilla, Carlos
    Britto, Ramona
    Bursteinas, Borisas
    Cowley, Andrew
    Da Silva, Alan
    De Giorgi, Maurizio
    Dogan, Tunca
    Fazzini, Francesco
    Castro, Leyla Garcia
    Figueira, Luis
    Garmiri, Penelope
    Georghiou, George
    Gonzalez, Daniel
    Hatton-Ellis, Emma
    Li, Weizhong
    Liu, Wudong
    Lopez, Rodrigo
    Luo, Jie
    Lussi, Yvonne
    MacDougall, Alistair
    Nightingale, Andrew
    Palka, Barbara
    Pichler, Klemens
    Poggioli, Diego
    Pundir, Sangya
    Pureza, Luis
    Qi, Guoying
    Rosanoff, Steven
    Saidi, Rabie
    Sawford, Tony
    Shypitsyna, Aleksandra
    Speretta, Elena
    Turner, Edward
    Tyagi, Nidhi
    BIOINFORMATICS, 2017, 33 (21) : 3454 - 3460
  • [10] UniProtKB/Swiss-Prot; How a protein knowledgebase can serve the medical community
    Estreicher, A.
    Bairoch, A.
    MOLECULAR & CELLULAR PROTEOMICS, 2006, 5 (10) : S65 - S65