3D Analog Library Generation Using Pubchem and Zinc

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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

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