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CPLM 4.0: an updated database with rich annotations for protein lysine modifications
- Source :
- Nucleic Acids Research
- Publication Year :
- 2021
- Publisher :
- Oxford University Press (OUP), 2021.
-
Abstract
- Here, we reported the compendium of protein lysine modifications (CPLM 4.0, http://cplm.biocuckoo.cn/), a data resource for various post-translational modifications (PTMs) specifically occurred at the side-chain amino group of lysine residues in proteins. From the literature and public databases, we collected 450 378 protein lysine modification (PLM) events, and combined them with the existing data of our previously developed protein lysine modification database (PLMD 3.0). In total, CPLM 4.0 contained 592 606 experimentally identified modification events on 463 156 unique lysine residues of 105 673 proteins for up to 29 types of PLMs across 219 species. Furthermore, we carefully annotated the data using the knowledge from 102 additional resources that covered 13 aspects, including variation and mutation, disease-associated information, protein-protein interaction, protein functional annotation, DNA & RNA element, protein structure, chemical-target relation, mRNA expression, protein expression/proteomics, subcellular localization, biological pathway annotation, functional domain annotation, and physicochemical property. Compared to PLMD 3.0 and other existing resources, CPLM 4.0 achieved a >2-fold increase in collection of PLM events, with a data volume of ∼45GB. We anticipate that CPLM 4.0 can serve as a more useful database for further study of PLMs.
- Subjects :
- Models, Molecular
AcademicSubjects/SCI00010
Protein Conformation
Lysine
Biology
Hydroxylation
medicine.disease_cause
computer.software_genre
Proteomics
Methylation
chemistry.chemical_compound
Annotation
Protein structure
Protein Interaction Mapping
Genetics
medicine
Database Issue
Animals
Humans
Biotinylation
RNA, Messenger
Phosphorylation
Databases, Protein
Internet
Mutation
Bacteria
Database
Ubiquitination
Proteins
RNA
Acetylation
Molecular Sequence Annotation
Plants
Subcellular localization
chemistry
Protein Processing, Post-Translational
computer
Software
DNA
Protein Binding
Subjects
Details
- ISSN :
- 13624962 and 03051048
- Volume :
- 50
- Database :
- OpenAIRE
- Journal :
- Nucleic Acids Research
- Accession number :
- edsair.doi.dedup.....77425fe89dfbef06a4b7eee533a52cfa