View source for 3D Analog Library Generation Using Pubchem and Zinc

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:

[[File:Screen_Shot_2018-05-07_at_12.00.26_PM.png|x500px]]




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

[[File:structure_search_selection_pubchem.JPG|x500px]]




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

[[File:Screen_Shot_2018-05-07_at_12.17.39_PM.png|x500px]]




We want to select the Identity/Similarity tab:

[[File:select_similarity_Search.JPG|x500px]]




That will bring up this screen:

[[File:Similarity search window.JPG|x500px]]




From here we want to select the CID, Smiles or InChl tab, paste in our smiles string, then we can select some parameters (Tanimoto greater than 0.80 and compounds only from ZINC):

[[File:Similarity search w parameters.png|x500px]]

[[File:Pubchem paramters for sim search.png|x500px]]





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

[[File:Tanimoto search output 2.png|x500px]]




We can select the following options from the resulting menu:

[[File:Strcutrue downlaod menu.JPG|x500px]]




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

[[File:Similarity search output.JPG|x500px]]




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.