Excuse me, I am learning how to do molecular docking and some targets I have docked have resulted with many favorable bonds but also with many unfavorable bonds in red. My question is, is there any criterion to know if the simulation, despite the unfavorable bonds, could allow molecular docking and induce or inhibit some biological mechanism? Thank you very much for your help.
yes, there will be always a possibility for the ligand to form weak bond interactions along with desired strong bond interactions, but it does not mean that the interactions formed during the molecular docking are irrelevant. but as always if you want to ensure that it is showing inhibition or not you need to validate the process by superimposing the existing reference molecules as standard with your hit molecule and then establish the interaction fingerprint. after this, you can proceed with Molecular dynamics simulation studies to validate the stability of the small molecule and protein complex.
hope it solves your doubts, good luck with your research :]
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