For example, two proteins are binding partners, how could we know that at which position or at which domain of one protein interact with its other partner protein. Need helps regarding any online software to sort out this problem.
If the structures or at least reliable homology models of the two proteins are available ( do a homology search on www.rcsb.org to find experimental structures), you can use protein-protein docking (e.g. http://zdock.umassmed.edu, https://haddock.science.uu.nl, https://cluspro.bu.edu/login.php, http://vakser.compbio.ku.edu/resources/gramm/grammx and others)
you can also try
http://milou.science.uu.nl/services/CPORT/
On the other hand, careful predictions are a good starting point for designing experiments able to confirm or disprove the prediction
Prediction can be done by homology modeling and docking, but this is only a prediction. If you want to know the exact interaction site, you must use structural biology techniques, including X-ray crystallography, NMR, and Cryo-EM. If you don’t have the resources or equipment, you can work together with a reliable partner to solve this problem. Recommend an article for you, maybe can help you choose an experimental method to determine the structure, https://www.creative-biostructure.com/comparison-of-crystallography-nmr-and-em_6.htm
Hope it helps!
Don't forget to check the uniprot record for your protein and it's ortholog in the nearest model organism - there may be some experimental evidence summarized there.
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