plmd Edit

Citations: 6

z-index: 6

Basic information
Short name plmd
Full name protein lysine modification database
Description PLMD (Protein Lysine Modifications Database) is an online data resource specifically designed for protein lysine modifications (PLMs)
URL http://plmd.biocuckoo.org
Year founded
Last update & version
Availability Free to academic users only
Contact information
University/Institution hosted Huazhong University of Science and Technology
Address Yongbo Xue Huazhong University of Science and Technology
City
Province/State
Country/Region China
Contact name Yongbo Xue
Contact email xueyu@hust.edu.cn
Data information
Object(s)
  • NA
Data type(s)
  • RNA
  • Protein
Data Category/Categories
  • Modification
Major organism(s)
  • Homo sapiens
Keyword(s)
  • PTMs
  • protein lysine modification
Publications
  • PLMD: An updated data resource of protein lysine modifications.[PMID: 28529077]
    Haodong Xu, Jiaqi Zhou, Shaofeng Lin, Wankun Deng, Ying Zhang, Yu Xue,

    Post-translational modifications (PTMs) occurring at protein lysine residues, or protein lysine modifications (PLMs), play critical roles in regulating biological processes. Due to the explosive expansion of the amount of PLM substrates and the discovery of novel PLM types, here we greatly updated our previous studies, and presented a much more integrative resource of protein lysine modification database (PLMD). In PLMD, we totally collected and integrated 284,780 modification events in 53,501 proteins across 176 eukaryotes and prokaryotes for up to 20 types of PLMs, including ubiquitination, acetylation, sumoylation, methylation, succinylation, malonylation, glutarylation, glycation, formylation, hydroxylation, butyrylation, propionylation, crotonylation, pupylation, neddylation, 2-hydroxyisobutyrylation, phosphoglycerylation, carboxylation, lipoylation and biotinylation. Using the data set, a motif-based analysis was performed for each PLM type, and the results demonstrated that different PLM types preferentially recognize distinct sequence motifs for the modifications. Moreover, various PLMs synergistically orchestrate specific cellular biological processes by mutual crosstalks with each other, and we totally found 65,297 PLM events involved in 90 types of PLM co-occurrences on the same lysine residues. Finally, various options were provided for accessing the data, while original references and other annotations were also present for each PLM substrate. Taken together, we anticipated the PLMD database can serve as a useful resource for further researches of PLMs. PLMD 3.0 was implemented in PHP + MySQL and freely available at http://plmd.biocuckoo.org.

    J Genet Genomics 2017:44(5)

    6 Citations (from Europe PMC, 2018-10-12)

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Record metadata

  • Created on: 2018-01-29
    • shireen huma [2018-04-12]
    • yang zhang [2018-01-28]

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