I notice when using SMILES or a IUPAC name for many molecules and generating them in Chembio3D, and then running MM2 > Minimize Energy, the structures produced are most of the time not reflections of any conformation observed physiologically.
I'm wondering if there's a way I can import protein and other macromolecules into Chembio3D, perhaps from a database somewhere, where I can view their precise arrangement either as found in crystallography or in vivo in their usual forms at physiological pH. Most importantly, the proteins would need to be accurate (something I find lacking when generating structures by name in chemdraw/chembio3d).
I appreciate that the proteins and other molecules are always changing conformation and interacting with other molecules, but at least a reasonable prediction of some realistic conformations to view them in 3D would be nice, instead of conformations that might rarely/never exist in a cell. Is this possible? And if so, how would I go about this? What would be the specific steps I need to follow to import these proteins into Chembio3D?