Difference between revisions of "3D Analog Library Generation Using Pubchem and Zinc"

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We can select the following options from the resulting menu:
We can select the following options from the resulting menu:
[[File:Strcutrue download menu.JPG|x500px]]
[[File:Strcutrue downlaod menu.JPG|x500px]]

Revision as of 14:01, 7 May 2018

Hello! This short write up is designed to make it easier for the group and other users that may stumble across this writeup curate a library of compounds analogous to compounds identified experimentally as active for the purpose of a secondary or follow-up virtual screen. First, we want a list of the actives compound's ZINC ID and smiles string. The example Il use here is ZINC000019831888 who's smile string is: OC(COC=1C=CC(=CC1)C(=O)C=2C=CC=CC2)CN3CCN(CC3)C=4C=CC=CC4Cl.

After collecting the pertinent information for the compounds were interested in, we can head to https://pubchem.ncbi.nlm.nih.gov This will bring up a screen that looks like this:

Screen Shot 2018-05-07 at 12.00.26 PM.png

We want to select the Structure Search bar on the right hand side of the screen:

Structure search selection pubchem.JPG

Then we are taken to this page: https://pubchem.ncbi.nlm.nih.gov/search/search.cgi

Screen Shot 2018-05-07 at 12.17.39 PM.png

We want to select the Identity/Similarity tab:

Select similarity Search.JPG

That will bring up this screen:

Similarity search window.JPG

From here we want to select the CID, Smiles or InChl tab, paste in our smiles string and search:

Smiles string pasted.JPG

A brief progress window will pop up followed, eventually, by a page specific to the query molecule:

Molecule title page.JPG

We can scroll down to section 5.2 and select the similar compounds tab:

Select similar componds from title page.JPG

This will bring up a screen like this and we can select structure download on the right hand side:

Structure download tab.JPG

We can select the following options from the resulting menu:

Strcutrue downlaod menu.JPG

Now, finally, we will generate some output that is a list of smiles strings of molecules analogous to the original query:

Similarity search output.JPG

From here, it would be best to copy and paste the resulting smiles strings into a text file for further manipulation. The next portion of this tutorial will deal with obtaining there dimensional structures from the 2 dimensional smile strings that were just obtained from Pubchem.