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Publication for RedoxDB
Features of reactive cysteines discovered through computation: from kinase inhibition to enrichment around protein degrons
[…] cysteine were returned, 540 of S-nitrosocysteine, and 66 of S-glutathionyl cysteine. Since the number of S-glutathionylation instances is relatively small, further data were sought and added from the redoxDB database (243 instances), and from proteomic studies (890 instances, and 353 instances), for a total of 1552. Filtering UniProt S-nitrosocysteine modifications for human leaves just 60 protein […]
Prediction of reversible disulfide based on features from local structural signatures
[…] e with similar flanking sequences (10 residues at both sides), the RevSS_PDB dataset consists of 230 reversible disulfides and 450 structural disulfides (Additional file : Table S1).To generate RevSS_RedoxDB dataset, we first retrieved 235 known reversible disulfides from the RedoxDB  which is a manually curated database for various types of experimentally validated redox-sensitve cysteines. We […]
SOHSite: incorporating evolutionary information and physicochemical properties to identify protein S sulfenylation sites
[…] ranscription factor H1F1A by SIRT6 . As shown in Table , the data were composed of 1443 positive and 10521 negative data on 987 S-sulfenylated proteins. An additional set of data was collected from RedoxDB , UniProtKB  and other published literature. From the RedoxDB database, we obtained 102 S-sulfenylated sites (positive dataset) in 92 proteins, while the rest of the cysteine residues in t […]
Quantitative H2S mediated protein sulfhydration reveals metabolic reprogramming during the integrated stress response
[…] niprot entry was searched and any annotation corresponding to the labeled cysteine peptides was collected.For redox cysteine annotation: each peptide identified by MS, all exact matches in any of the RedoxDB databases on any oxidative modification cysteine sequences (fasta or additional_fasta) were collected. For motif search: The lager data set of putative modification cysteine sites and their vi […]
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