I have a protein sequence with two cysteine residues and I would like to predict if those cysteins will form disulfide bonds.
I am looking for user-friendly tools to do this, either online tools or some other kind of easy to use software, since I am not well-versed in bioinformatics.
Hi!
I know this webserver - CYSPRED
http://gpcr.biocomp.unibo.it/cgi/predictors/cyspred/pred_cyspredcgi.cgi
There are a bunch of machine-learning-prediction methods available (Article diSBPred: A Machine Learning based Approach for Disulfide Bo...
), but I am not very sure how accurate their predictions are. An optimal way to address your problem is to first see if there are any available 3D structures for your protein sequence. You can perform a BLAST against the PDB database and check the results. If you don't find an exact match, but do see a lot of homologs from BLAST, having (let's say) >60% sequence identity and >90% query coverage, then you can predict the 3D structure using I-Tasser (https://zhanggroup.org/I-TASSER/). Once you have the 3D structure of your protein, you can then use this server -Article Disulfide by Design 2.0: A web-based tool for disulfide engi...
to check for potential disulfide bonds.
If the structure of your protein is not known, look into similar proteins. It might be the case that dimerization or some other association is nearly always the case. Then you can model/compare your protein to see where the cysteine residues reside and even if they can form disulfide bonds.
1. http://scratch.proteomics.ics.uci.edu/
1a. http://scratch.proteomics.ics.uci.edu/explanation.html#DIpro
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