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How to search DTP/NCI Compounds

posted Apr 8, 2016, 9:35 AM by Dong Xu   [ updated Sep 5, 2016, 2:34 PM ]
An easier option is to use Enhanced NCI Database Browser 2.2

https://cactus.nci.nih.gov/ncidb2.2/

In Query Data Value, paste SMILES string and set Tc threshold.

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1. If you have a ZINC ID, go to http://zinc15.docking.org and then "substance", enter ZINC ID to locate the compound.
2. Copy the "InChI" code, not SMILES, not "InChI Key"
3. Go to https://pubchem.ncbi.nlm.nih.gov/#  Click "Structure Search" on the rght
4. Click "Identity/ Similarity" -> "CID, SMILES, InChI"
5. Paste the "InChI" code
6. Options: You can choose Identical or vary similarity threshold 80, 90, 95%
7. Click Filter -> Data Source From, choose "DTP/NCI". Once you selected this once, it will pop into  Compound Subset under Filter to be used later. This is a critical step if you want only DTP/NCI compounds
8. Click Search and get results
9. Pick the compounds that starts with NSC numbers
10. Take the NSC numbers and check against DTP/NCI database at https://dtp.cancer.gov/dtpstandard/dwindex/index.jsp

Note: based on what you want, varying similarity threshold may give you more compound options.

All DTP/NCI compounds sdf file can be downloaded from here https://cactus.nci.nih.gov/download/nci/
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