Hello dear researchers,
I would like to know about available in silico tests that could predict the activity of ligands (small molecules) against the target protein.
- I have performed docking and obtained the affinity and followed by MDS for 100ns for 4-5 complexes and all the ligands fall under stable RMSD/RMSF/RG values and energy ranges of simulations are aligning with the average values mentioned in the description of gromacs energy module.
What techniques should be now carried out to know if these compounds perform inhibition/activation or are they merely substrates of these targets?
- would you suggest umbrella sampling or streered MD or such enhanced sampling methods or are there any definitive methods?
Thank you,
Regards,
Sandra
Sandra Jose
You could be validated your targeted complexes using MMGB/PBSA of simulated trajectories and proposed robust results.
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Hello Waseem, thanks for your answer!
MMPBSA is more or less talking about the binding energy, but my question is regarding the activity, not energy.
I have done mmpbsa already.
Sandra
Activity is a reaction, which happens when there is a exchange of electrons, classical all atom simulation wont be able to predict the exchange, which is at a sub atomic level. For that you must read about Hybrid (QM/MM) simulations, and that might give you the real insights, only if you have a x-ray crystal structure of the docked pose your protein and ligand of interest.
Diptesh
Answer in your question .If you perform docking with validation its perfect. ligand dock with protein and good binding score that at first step reflect ligand have activity but human body complex thus molecular dynamic supports our work.
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