Could you please list some common methods for identifying the binding pocket? I mean we have a compound and a protein of interest, so which domain of the protein will be binding with the compound? And my major is molecular biology. How can I verify the binding pocket with the methods in my field? Thank you very much!!
1. U need to go back to the literature to find out the catalytic n mechanism of action of the proteins you are targeting
2. Also u could check the active residue participating in interaction (using pymol) of existing drugs to get an idea of the binding or catalytic pocket
3. U can also target allosteric sites
4. Nowadays most of the paid softwares like Schrodinger maestro modules automatically predicts the possible binding pocket n allosteric sites. Most of the free servers also does the same but are not reliable, afterall u need to convince the reviewer as well. If you are using free softwares u may follow option 1 n 2
You've to be ble to analyse 3-D characteristics of both receptor & ligand and bond attractions which is very complex info, only known by very few highly trained chemists with high salaries and million usd bonuses work in pharma industries. But be sure almost nobody teaches these info to anyone since millions of usd gain, therefore you have to learn yourself if you are capable enough to learn !
Hi,
A method that you could consider is hydrogen-deuterium (H/D) exchange mass spectrometry. This allows you to monitor overall exchange of protein backbone amide hydrogens in the free protein versus that in the protein bound to your small molecular drug. In many cases, the exchange is impaired/hampered in the regions where the protein interacts with the ligand, pointing you to the area of the protein that is involved in binding.
It is not the easiest of methods, but might be worth a shot!
Hi Mingqi Li ! This is an interesting and difficult problem, but fortunately there are lots of methods you can try to make progress. First, to identify possible binding sites you can try these steps:
After identifying these pockets, you’ll need to perform experiments in your lab to validate these interactions using techniques common in molecular biology, such as site-directed mutagenesis or Isothermal Titration Calorimetry (ITC).
Good luck with your research!
Here are two tools to get you started:
1. https://cadd.labshare.cn/cb-dock2/php/index.php
2. http://www.pkumdl.cn:8000/cavityplus/index.php
PS: You should consider the above comments if you are going for a specific active/allosteric site.
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