[Chimera-users] chemdraw addins

Elaine Meng meng at cgl.ucsf.edu
Wed Aug 31 17:17:46 PDT 2011

Hi Bill,
Thanks for the kind words!

There is no Chemdraw input, but you can input a PubChem CID (compound identifier) or a SMILES string to generate a reasonable 3D structure of the compound.  This is done using a web service at Indiana U. (requires being connected to the internet). These structures have already passed through a minimization process.  The Build Structure tool (under Tools... Structure Editing in the menu), Start Molecule tab, includes these options,
and the PubChem fetch is also available in the Fetch by ID dialog (in the main File menu).

Chimera does not do automatic docking, but you can "dock" manually by activating/deactivating structures, in other words, freezing one in place so that the mouse only moves the other one, as described here:

Manual placement can be difficult.  If the ligand in the crystal structure is quite similar to the ligand you want to model, there are at least two more possibilities:

(a) just use the Build Structure tool, Modify Molecule tab, to change the structure of the existing ligand

(b) open the new ligand structure, then use the "match" command to superimpose its atoms with the corresponding atoms of the existing ligand.  Then you can delete the old ligand from the original structure.  

Be aware that minimization really has very limited ability to predict conformation changes upon binding.  The structure will only sink to the nearest minimum (will not cross energy barriers), possibly getting trapped in a strained conformation.  It won't move very far.  You can also try interactively rotating bonds in the ligand and receptor
or if the receptor is a protein, replacing the current conformation of an amino acid sidechain with a different rotamer

I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Aug 31, 2011, at 2:07 PM, Bill Wuest wrote:

> Hi,
> I am a big fan of your software and would like to use it in greater capacities (primarily for drug discovery). Is there a way to dock molecules (or better yet import chemdraw files) into chimera and then swap those structures in for ligands bound to crystal structures? I would like to model proposed compounds into a binding site of a protein and riboswitch both of which have the ligand bound in the crystal structure. Ideally I would like to import a chemdraw file which could be minimized by chimera and then be able to limit the docking to the ligand binding area and minimize again. That way I can see how the new analog changes the conformation of the protein. Any help would be greatly appreciated! If it would be easier to chat on the phone please feel free to call the number below. Have a great week!
> -Bill Wuest

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