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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?

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  • $\begingroup$ A side question, can you alter bond angles in ChemBio3D? $\endgroup$ – Melanie Shebel Apr 19 '15 at 16:28
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The site you are looking for is the Protein Data Bank.

You can get to it with one of these links.
www.wwpdb.org
www.pdbe.org
www.rcsb.org/pdb
www.pdbj.org

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    $\begingroup$ Short and to the point. :) Might be better to link to the actual page, rcsb.org/pdb/home/home.do and not the Wikipedia page. $\endgroup$ – Jun-Goo Kwak Apr 19 '15 at 5:05
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    $\begingroup$ @Jun-GooKwak There are 3 links on the Wikipedia page, depending on the organization that accesses the information. $\endgroup$ – LDC3 Apr 19 '15 at 13:41

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