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PLMD specifications

Information


Unique identifier OMICS_18707
Name PLMD
Alternative name Protein Lysine Modification Database
Restrictions to use None
Database management system MySQL
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained Yes

Subtools


  • CPLA
  • CPLM

Maintainers


  • person_outline Yu Xue
  • person_outline Dr. Zexian Liu

Additional information


http://plmd.biocuckoo.org/userguide.php

Publications for Protein Lysine Modification Database

PLMD citations

 (6)
library_books

Improving succinylation prediction accuracy by incorporating the secondary structure via helix, strand and coil, and evolutionary information from profile bigrams

2018
PLoS One
PMCID: 5809022
PMID: 29432431
DOI: 10.1371/journal.pone.0191900

[…] The benchmark dataset was extracted from the Compendium of Protein Lysine Modifications (CPLM) [, ]. This compendium consists of over 45,000 proteins from 122 species, and 12 different annotated PTMs. In the CPLM, succinylation was the most abun […]

library_books

The first succinylome profile of Trichophyton rubrum reveals lysine succinylation on proteins involved in various key cellular processes

2017
BMC Genomics
PMCID: 5545033
PMID: 28778155
DOI: 10.1186/s12864-017-3977-y

[…] hen translation is occurring. Additionally, the succinylated sites on core histones were different between the conidia and mycelia stages, and the succinylated site H4K60 has not been reported in the CPLM database to date.Succinylation is regulated by two types of enzymes with opposing activities, lysine succinyltransferase and desuccinylases. So far no enzyme that catalyze succinylation and desuc […]

library_books

Frequent mutations in acetylation and ubiquitination sites suggest novel driver mechanisms of cancer

2016
Genome Med
PMCID: 4864925
PMID: 27175787
DOI: 10.1186/s13073-016-0311-2

[…] ted as PTM enzymes. Interactions for acetylation and ubiquitination were compiled separately. PTM enzymes were curated from three resources: the Gene Ontology [], the hUbiquitome database [], and the Compendium of Protein Lysine Acetylation (CPLA) []. Survival information of patients profiled by the TCGA were retrieved from the study by Kandoth et al. []. Patients with each type of cancer were ana […]

library_books

The interplay of post translational modification and gene therapy

2016
Drug Des Devel Ther
PMCID: 4778776
PMID: 27013864
DOI: 10.2147/DDDT.S80496

[…] lysine modifications include butyrylation, propionylation, malonylation,, crotonylation, and succinylation. Currently, there is the provision of a compendium of protein lysine modification database (CPLM) updated from a previously developed compendium of protein lysine acetylation (CPLA). The authors revealed that manual collection of experimentally identified substrate and sites was carried out […]

library_books

Proteome wide analysis reveals widespread lysine acetylation of major protein complexes in the malaria parasite

2016
Sci Rep
PMCID: 4728587
PMID: 26813983
DOI: 10.1038/srep19722

[…] ing the previous sites reported in P. falciparum and comparing the merged dataset with the histone acetylation sites present in H. sapiens, S. cerevisiae, D. melanogaster and M. musculus by using the CPLM database. […]

library_books

Accurate in silico identification of species specific acetylation sites by integrating protein sequence derived and functional features

2014
Sci Rep
PMCID: 4104576
PMID: 25042424
DOI: 10.1038/srep05765

[…] Annotations of lysine acetylation sites were extracted from multiple public resources. These include CPLA (http://cpla.biocuckoo.org/), N-ACE (http://N-Ace.mbc.NCTU.edu.tw/), Phosida (http://www.phosida.com/), ASEB (http://cmbi.bjmu.edu.cn/huac) and PhosphoSitePlus (http://www.phosphosite.org). Among […]

Citations

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PLMD institution(s)
Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology and the Collaborative Innovation Center for Brain Science, Huazhong University of Science and Technology, Wuhan, China
PLMD funding source(s)
Supported by grants from the National Basic Research Program (973 project) (No. 2013CB933900), Natural Science Foundation of China (Nos. 31671360 and J1103514), and International Science & Technology Cooperation Program of China (No. 2014DFB30020).

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