Jun 7, 2010

Aligning Small Molecules

From there:  to here:

Aligning two small molecules is useful and necessary when studying the similarities of form and character of two distinct molecules. Here's one way of doing that in PMV.


2. Select ADD PAIRS.

3. Turn the  BY STRING mode on. You could do this by picking atoms by hand as well. But I find the selecting by string is faster if your molecules have enough similar points (3).

4. The two molecules that I am aligning are methionine and glutamate. I know that they share at least their backbone atoms and the beta carbon "CB". All I need is 3 atoms for an alignment, so I just type "backbone" under the ATOM heading for the REFERENCE and MOBILE nodes. Note that the reference molecule will stay put, while the mobile molecule will be aligned onto the reference molecule, as you might expect.

Also note that by clicking SHOW you will see little blue and red stars over the reference and mobile atoms.

Click OKAY.

5.  Now click CREATE PAIRS  in the superimpose window.

 6. Your molecules should be aligned and you can  DISMISS the "pairwise superimposition" window.

Have fun, 


Anonymous said...

Thanks for this tip. There are other ways to align small molecules that are easier and that will return quantitative information. For example, YASARA-Structure will automatically align molecules and return the RMSD of the paired atoms. vROCS (OpenEye software) will align molecules and return Tanimoto coefficients for shape and "color" (pharmacophore matching).

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