Hello everyone.
As you know, we can download 3D structures of molecules from PubChem. On the other hand, there is a wide range of molecular docking software, such as discovery studio and maestro, in which we can prepare our interest molecule in 3D format. When I compare the RMSD of the molecule that I downloaded from PubChem with a molecule that has been prepared by maestro there is a bit difference between them. Now, which structure should be a reliable reference for me?
Are PubChem 3D structures more accurate than other 3D structures optimized by different software?
I just want to make sure that preparing ligands using maestro give me precise structures.
Any help is highly appreciated.
You may want to read this:
Article PubChem3D: Conformer generation
It is expected to have change(s) in ligand conformation after preparation in any software. If no changes, of what essence is the "preparation"? In the case of maestro ligand preparation panel, several parameters are definitely checked either by choice or default and resulting conformers come in different tautomers depending on your configuration in the panel. These parameters help to "better" the original 3D structure downloaded from any database (e.g pubchem) because some these compounds might have invalid dihedral bonds, bond angles and torsional bonds etc . I'll suggest you have enough understanding of each parameters you're considering in maestro before "preparation".
Yes, your final structure is better than the imported one depending on your configuration.
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