Dear colleagues, I've got a list of molecules (just names) which I would like to convert into a library for virtual screening. So, I wonder what is the most convenient way to get the structures (2D or 3D) when one has only the names? Of course, one can write them by hand, but it can be hardly done for hundreds and thousands of molecules. Is there any soft able to recognize the chemical names and help me to proceed with this task? Would be grateful for any suggestions.
Hi Sergii,
You can extract 2D or 3D structures from the following database by use of, for example, a shell script:
http://www.cureffi.org/2013/10/04/list-of-fda-approved-drugs-and-cns-drugs-with-smiles/
http://drugcentral.org/download
http://chemoinfo.ipmc.cnrs.fr/download.html
https://www.researchgate.net/post/FDA_approved_drugs_in_SDF_format
Dear colleagues, thank you very much for your helpful suggestions and links provided!
If you mean IUPAC name to structure, there is OPSIN.
OPSIN - Open Parser for Systematic IUPAC Nomenclature
- web service https://opsin.ch.cam.ac.uk/
- source code https://bitbucket.org/dan2097/opsin/src
You can use KNIME analytics platform and the attached Knime node (CIR - chemical identifier resolver) based on NIH/NCI Chemical Identifier Resolver (https://cactus.nci.nih.gov/chemical/structure). Just copy the attached jar file in KNIME\dropins folder.
You can use ChemDraw software to convert the name of molecule to its structure.
Hi!
I recommen you to use JChem for excel (ChemAxon)
If you have IUPAC names or similar, it will convert the list into structures with the option "from any text". Then, you can export a combined file (.sdf) or several files with the structures or transform them into smiles, whatever you need.
Thanks everyone for the valuable suggestions! I tried different approaches and revealed that JChem and ChemDraw are the best solutions currently. Both of them have plugins for the MS Excel, so they are suitable for the fast conversion of whole text libraries into structural libraries. They can even convert such complicated names as "3beta-Hydroxy-4beta-methyl-5alpha-cholest-7-ene-4alpha-carbaldehyde", so I am happy with their work.
CIR KNIME node is now available directly in KNIME, see instructions here:
https://bit.ly/3lfuP2p
See also our project on ResearchGate:
https://www.researchgate.net/project/KNIME-nodes-for-curation-of-chemical-datasets
There are some ez ways like searching the compounds names in chemical databases like PubChem and Chemspider and download their respective sdf or pdb files. Next, you can simply open those files with a text- editing tools like notepad. Once you have opened them, copy the entire text in the each file into one new text document. After that, just change the file format from .txt to .sdf or .pdb. In this ez way you will have all the compounds in one file.
In an other way, drag all the compounds' file into the OpenBabl software's input query and convert to what format you wish. The resulted file will contain all your data.
Hi. I am using the CIRpy library and have done so for the past few years, but now the resolver it uses (http://cactus.nci.nih.gov/chemical/structure) it appears to be down. I wonder whether any of you has some suggestion about how to use, eg, the Pubchem resolver within a Python script as an alternative when the Cactus link is down?
Hi Andrea,
I put that advice to good use today. However it doesn't seem I can get the CAS number with PubChemPy, right?
Hi Driss,
I already have my CIRpy script that extracts the CAS number. But I'm currently writing a PubChemPy script as a backup when the CIRpy server is down. And it seems that PubChemPy doesn't extract the CAS number.
Hi Théophile Gaudin I am sorry but didn't develop CIRpy so I cannot help you.
Best regards,
Andrea
Hi Théophile Gaudin I am sorry but didn't develop CIRpy so I cannot help you.
Best regards,
Andrea
Hi Théophile Gaudin I am sorry but didn't develop CIRpy so I cannot help you.
Best regards,
Andrea
Hi Théophile, I am sorry but didn't develop PubChemPy so I cannot help you.
Best regards,
Andrea
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