Protein-protein interaction prediction
protein-antibody interaction prediction
protein-glycans interaction prediction
It certainly depends on what kind of interactions you're looking for.
As has been already mentioned, there are options for prediction by protein docking. You can use ZDOCK online (http://zdock.umassmed.edu/) but even that software is limited by the availability of protein structures. I also found the PRISM server (http://cosbi.ku.edu.tr/prism/) recently but haven't tried it yet.
Sometimes it's easiest just to check on proteins in the STRING database first (http://string-db.org/) - most of its interactions are really just predictions. I'm also familiar with iLoops (http://sbi.imim.es/iLoopsServer/). It doesn't require a structure but just makes feature-based predictions.
A number of tool servers unfortunately only do predictions for common model organisms (i.e., yeast) so hopefully that doesn't matter for you.
Thank you for your suggestions. I am trying to do trimeric protein and antibody interactions.
One more suggestion which may be more relevant to the multimer interactions, at least: COTH (http://zhanglab.ccmb.med.umich.edu/COTH/).
Which bioinformatics software is best out there to predict antigenic epitopes from a protein sequence?
- Badges
- Science topic
- Similar topics
- Geoscience
- Asia
- India