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Protocols

SysPTM specifications

Information


Unique identifier OMICS_06899
Name SysPTM
Interface Web user interface
Restrictions to use None
Input data A protein name or protein SwissProt AC or ID.
Computer skills Basic
Version 2.0
Stability Stable
Maintained No

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Publications for SysPTM

SysPTM citations

 (11)
library_books

A validated antibody panel for the characterization of tau post translational modifications

2017
Mol Neurodegener
PMCID: 5697095
PMID: 29157277
DOI: 10.1186/s13024-017-0229-1

[…] including the Human Protein Reference Database (HPRD 9.0), the Phospho.ELM database (PhosphoELM.10011), PhosphoSitePlus (Phosphositeplus.1010730), UniProtKB/Swiss-Prot (Phosphositeplus.1010730), and SysPTM (SysPTM 1.1). We used the Uniprot ID: P10636 to query dbPTM for microtubule-associated protein tau (MAPT) entries, and mapped the modified residue positions to the PNS-tau isoform and then to t […]

library_books

BioMuta and BioXpress: mutation and expression knowledgebases for cancer biomarker discovery

2017
Nucleic Acids Res
PMCID: 5753215
DOI: 10.1093/nar/gkx907

[…] tained through retrieval and mapping of UniProtKB feature (FT) lines (see for a list of all FT entities used in functional annotations). Additional sources of functional annotations include: CDD (), SysPTM 1.1 (), PhosphoSite (), Phospho.ELM (), dbSNO 1.0 (), HPRD 9.0 () and OGlycBase6.0 ().Finally, all variation entries were unified to Disease Ontology or DO () terms to facilitate better cancer […]

call_split

Prediction of post translational modification sites using multiple kernel support vector machine

2017
PeerJ
PMCID: 5410141
PMID: 28462053
DOI: 10.7717/peerj.3261
call_split See protocol

[…] s (phosphorylation, O-linked glycosylation, acetylation) collected from several major comprehensive PTM databases, including dbPTM (version 3.0) (), PhosphoSitePlus (), Phospho. ELM (), dbOGAP () and SysPTM (). The detailed information of this dataset was provided in . For Y sites, we followed the procedure described in and collected 1,791 local sequences (containing phosphorylation, sulfation an […]

library_books

GlycoMinestruct: a new bioinformatics tool for highly accurate mapping of the human N linked and O linked glycoproteomes by incorporating structural features

2016
Sci Rep
PMCID: 5052564
PMID: 27708373
DOI: 10.1038/srep34595

[…] The annotations of C-, N-, and O-linked glycosylation sites were extracted from four major public resources, including UniProt, PhosphoSitePlus, SysPTM, and O-GlycBase (version 6.0). Only experimentally verified glycosylation sites in the human proteins were retained. To ensure the quality of the curated datasets, any glycosylation sites annot […]

library_books

Nonsynonymous Single Nucleotide Variations on Some Posttranslational Modifications of Human Proteins and the Association with Diseases

2015
PMCID: 4606098
PMID: 26495027
DOI: 10.1155/2015/124630

[…] The eight human PTM data sets of Phosphorylation, Ubiquitylation, Acetylation, Glycosylation, Methylation, SUMOylation, Hydroxylation, and Sulfation were obtained from SysPTM 2.0 (released in June, 2013) [], which integrated PTMs from public resources as well as manually curated MS/MS identified PTMs from experimental research articles, and dbPTM 3.0 (released in Ju […]

library_books

Human germline and pan cancer variomes and their distinct functional profiles

2014
Nucleic Acids Res
PMCID: 4191387
PMID: 25232094
DOI: 10.1093/nar/gku772

[…] vailable databases and generates a data set containing only experimentally verified entries, which include data from UniProtKB/Swiss-Prot, Phospho.ELM (), PhosphoSitePlus (), O-GLYCBASE (), dbSNO (), SysPTM () and HPRD (). However, heterogeneity issues still left unresolved include (i) annotations are not mapped to a unified proteome reference and (ii) naming of PTMs is not standardized. In this s […]

Citations

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SysPTM institution(s)
Key Laboratory of Biomedical Photonics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China; Shanghai Center for Bioinformation Technology, Shanghai Institutes of Biomedicine, Shanghai Academy of Science and Technology, Shanghai, China; Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China; Department of Bioinformatics and Biostatistics, Shanghai Jiaotong University, Shanghai, China; Key Laboratory of Systems Biology, Chinese Academy of Sciences, Shanghai, China; Proteome Center Rostock, Department for Proteome Research, Institute of Immunology, University of Rostock, Rostock, Germany
SysPTM funding source(s)
Supported by Ministry of Science and Technology of China [2010CB912702, 2012AA020409, 2012AA020201, 2011CB910204]; the National Natural Science Foundation of China [81201666, 31070752]; the Key Infectious Disease Project [2012ZX10002012-014], and the EU-funded KRAB-ZNF IRSES project (269 186).

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