Hi guys,
I have a question related to structure-based (SB) pharmacophore modeling using LigandScout. There is no PDB file for complex of protein and ligand of interest. In this situation I cannot do SB? Can I use docked complexes instead of PDB files? Or it is better to do ligand-based pharmacophore modeling?
Any help would be greatly appreciated.
Samane
Hi Samaneh,
As you mentioned, the X-ray crystal structures of protein-ligand complexes are not available in Protein Data Bank for your target, therefore, I suggest you to opt for Ligand based pharmacophore modelling approach. Then, you may perform molecular docking to analyse protein-ligand interactions. Hope this would help you.
Many thanks dear Arun.
Since structure based pharmacophore modelling is more accurate than ligand based, I thought it may be possible with docked complexes. I go for ligand based.
It depends on how confident are you about your docking model. If the target is a representative of a well-studied (and well behaved) protein family, e.g., a kinase, you can give it a try. Anyway, it would not be more risky than a ligand-based pharmacophore. If you are undecided, you should try both ligand- and structure-based pharmacophores.
thank you for your reply. Since different docking software dont give the similar results, I think it is better to go for ligand based pharmacophore. Currently I have problem in deriving each of models, ligand and structure based. I am going to use ligandScout, but in evaluation version, conformer generation is not active. Any comment would be appreciated.
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