Hello, is it possible to fix atoms in ligand in Maestro Schrodinger during the docking? There is well known it's simple by the protein/enzyme, I mean to show/ to select which must interact in docking. Even better is Maestro able to create special "interaction" between selected atoms in Ligand and Protein?
Thank you for the answers but I for example:
I have a metal atom in the active centre of enzyme. I dock the ligand with carboxyl group. I want the ligand to interact by the two oxigen atoms from carboxyl group. Maestro is docking by showing the interaction with one (which is possible as well) but it is not prefered for this type of enzyme and inhibitors. I want to fix interaction of two oxigens and metal.
That is what distance constraint is. You define two atoms and approximate distance between them so that docking program will be forced to place those two atoms in that distance range. It is widely used in molecular dynamics and NMR structure optimization. In docking, it is rarely used. PatchDock allows such constrains. No provisions in AutoDock 4 or vina so far. I am not sure about Maestro. You may try molecular dynamics though, with restraints on those atoms. In maestro you can modify the docked complex by dragging the atoms and placing them at the desired location. So, one way to achieve it would be to modify the coordinates and then running the dynamics.
There is a function called "core constraint" in Glide (that is, Maestro's docking algorithm). To use it, you need (i) to dock and adjust some sample ligand containing a given structural core to the protein of interest, and (ii) specify the core structure. Then, all ligands containing that core would be docked in the same way as the sample ligand was.
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