The interaction between drug target and ligand (drug) was performed with the help of biotools or online server(autodock or swissdock). After successful docking, how you can predict desired activity (activator or Inhibitor) drug like molecules by using in silico approach. Suggest some tools for that.
Depends on the software, previous reports criteria etc. There are some software which identify the inhibitor/activator and based on their scoring, one such is PASS.
I dont think any program can give you such information without introducing reference bioactive compounds to the database eg. activators and Inhibitors...
Software/algorithm can only tell about binding pose. To some extent binding affinity. Not inhibition or activation.
I think MDS can solve the puzzle... But it uses quite a number of algorithms
@naruka - can you elaborate your view on MD to differentiate activator and inhibitor?
I agree with Anu Manhas the in vitro study must be done to confirm the in silico results.
Talia Serseg But you are going to fix the docking site. So you cant expect that it wont bind
Joel Subach What analysis in MD will help in differentiating activator and inhibitor?
Mahadev Asaram Jadhav There are many drug property prediction tools both in linux and windows OSs. Try some tools like admetSAR and others to know their mechanism of action.
At the end, docking results are always confirmed by in-vitro experiemnts whether it is activating or inhibiting the activity. I also agree with the above answers
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