Chen's data sets have been integrated!!!

A total of 174 experimentally verified S-nitrosylation sites on 94 S-nitrosylated proteins from individualized human colorectal cancer tissues using a label-free quantitation strategy. (Chen et al., 2014) have been integrated into dbSNO 2.0.

Disease databases will be annotated on dbSNO 2.0!

We integrate the three Disease database, users can investigate more diaease annotated for S-nitrosylation in dbSNO 2.0.

1. OMIM database : Online Mendelian Inheritance in Man. OMIM Database  [PubMed]
2. KEGG database : Kyoto Encyclopedia of Genes and Genomes.(Diseases viewed as perturbed states of the molecular system) KEGG Database  [PubMed]
3. HPRD database : Human Protein Reference Database. HPRD Database  [PubMed]

PSICQUIC molecular interaction databases will be annotated on dbSNO 2.0!

PSICQUIC is an effort from the HUPO Proteomics Standard Initiative (HUPO-PSI) to standardise the access to molecular interaction databases programmatically. PSICQUIC integrate many protein-protein interaction database. (APID, BAR, bhf-ucl, BIND, BindingDB, BioGrid, ChEMBL, DIP, DrugBank, GeneMANIA, HPIDb, I2D, I2D-IMEx, InnateDB, InnateDB-IMEx, IntAct, Interoporc, iRefIndex, MatrixDB, MBInfo, mentha, MINT, MolCon, MPIDB, Reactome, Reactome-FIs, Spike, STRING, TopFind, UniProt, VirHostNet).

We integrate the PSICQUIC database, users can investigate more protein-protein interaction for S-nitrosylation in dbSNO 2.0. PSICQUIC Database  [PubMed]

The S-nitrosylation sites in the PubMed database on 2014 research articles is integrated in dbSNO 2.0!

1. Sehrawat A et al. (2014) "S-Nitrosylation Analysis in Brassica juncea Apoplast Highlights the Importance of Nitric Oxide in Cold-Stress Signaling.", Journal of proteome research, Vol. 13(5):2599–2619. [PubMed]
2. Qu Z et al. (2014) "Proteomic Quantification and Site-Mapping of S-Nitrosylated Proteins Using Isobaric iodoTMT Reagents.", Journal of proteome research, Vol. 13(7):3200-11. [PubMed]
3. Lee YI et al. (2014) "Protein microarray characterization of the S-nitrosoproteome.", Molecular & cellular proteomics, Vol. 13(1):63-72. [PubMed]
4. Zareba-Koziol M et al. (2014) "Global analysis of S-nitrosylation sites in the wild type and APP transgenic mouse brain- clues for synaptic pathology.", Molecular & cellular proteomics. [PubMed]

KEGG(Kyoto Encyclopedia of Genes and Genomes) pathway will be annotated on dbSNO 2.0!

We integrate the KEGG pathway database, users can investigate more signaling pathway for S-nitrosylation in dbSNO 2.0. KEGG Pathway Database

PDB(Protein Data Bank) structural will be annotated on dbSNO 2.0!

We integrate the RCSB Protein Data Bank, users can investigate more protein structural for S-nitrosylation in dbSNO 2.0. RCSB Protein Data Bank(PDB)

The S-nitrosylation sites in the PubMed database on 2013 research articles is integrated in dbSNO 2.0!

1. Maron BA et al. (2013) "S-nitrosothiols and the S-nitrosoproteome of the cardiovascular system.", Antioxid Redox Signal, Vol. 18(3):270-87. [PubMed]
2. Camejo D et al. (2013) "Salinity-induced changes in S-nitrosylation of pea mitochondrial proteins.", Journal of proteomics, Vol. 79:87-99. [PubMed]
3. Doulias PT et al. (2013) "Site specific identification of endogenous S-nitrosocysteine proteomes.", Journal of proteomics, Vol. 92:195-203. [PubMed]
4. Ratnayake S et al. (2013) "Stabilising cysteinyl thiol oxidation and nitrosation for proteomic analysis.", Journal of proteomics., Vol. 92:160-70. [PubMed]

The S-nitrosylation sites in the PubMed database on 2012 research articles is integrated in dbSNO 2.0!

1. Li BQ et al. (2012) "Predict and analyze S-nitrosylation modification sites with the mRMR and IFS approaches.", Journal of proteomics, Vol. 75(5):1654–65. [PubMed]
2. Scheving R et al. (2012) "Protein S-nitrosylation and denitrosylation in the mouse spinal cord upon injury of the sciatic nerve.", Journal of proteomics, Vol. 75(13):3987-4004. [PubMed]
3. Foster MW et al. (2012) "Proteomic characterization of the cellular response to nitrosative stress mediated by s-nitrosoglutathione reductase inhibition.", Journal of proteome research, Vol. 11(4):2480-91. [PubMed]
4. Murray CI et al. (2012) "Identification and quantification of S-nitrosylation by cysteine reactive tandem mass tag switch assay.", Molecular & cellular proteomics, Vol. 11(2):M111.013441. [PubMed]

Bioinformatics advance access published July 10, 2012

Lee TY, Chen YJ, Lu CT, Ching WC, Teng YC, Huang HD, Chen YJ. (2012) "dbSNO: a database of cysteine S-nitrosylation.", Bioinformatics, Vol. 28(17):2293-5. [PubMed]

Chen's data sets have been integrated!!!

A total of 586 experimentally verified S-nitrosylation sites from SNAP/L-cysteine-stimulated mouse endothelial cells (Chen et al., 2010) have been integrated into dbSNO.

Protein disorder region will be annotated on dbSNO!

It was proposed that protein modification is associated with the protein disorder region. Thus, we integrate the protein disorder prediction tool, DISOPRED 2, to comprehensively annotate the protein entries in dbSNO. Users can investigate more structural information for protein modifications.

The S-nitrosylation sites in UniProt is integrated in dbSNO!

A total of 37 experimentally verified S-Nitrosylation sites in UniProt release 2011-06 were integrated.

The orthologous conserved region of protein sequences is considered!

In order to observe whether a PTM sites located in the conserved regions of protein orthologous sequences, the Clusters of Orthologous Groups of proteins (COGs), was integrated. The alignment of the protein sequences in each cluster, which was implemented by ClustalW, is provided in the resource.

dbSNO 1.0 is starting up!

dbSNO is a knowledge base comprising the experimental S-Nitrosylation sites, solvent accessibility of substrate, protein secondary and tertiary structures, protein domains and protein disorder. Literature related to PTM, protein conservations and substrate specificity are also analyzed. The interface is also redesigned and enhanced to facilitate access to the resource.