PubChem Online Compound Search and Download
Hi All, I have been using the PubChem database to search for uncharged small molecules. However, even after specifying zero charge, PubChem still outputs compounds containing amino groups (-NH2) and carboxylic acids (-COOH); since I am interested in physiological pH, these compounds would actually be charged. Is there some way to exclude molecules containing these functional groups? I've noticed that there is an option on PubChem to include only certain atoms, but the search times out at 2 minutes if I try this. I'd like to exclude halogens and aldehydes as well, can this be specified? Finally, after searching for numerous compounds, how could all of them be downloaded into an organized compound library? If there is another online compound database besides PubChem that can be easily searched and has the same or better functionality, I'd greatly appreciate any info about it. Thanks, Nancy
Dear Nancy, I don't know how Pubchem works but I think that you should try to use ZINC database (zinc.docking.org) which has implemented a large number of filters (pH, toxic functional groups, etc) and the selected compounds can be downloaded as a compound library. Best regards, Aldo -- ========================================= Aldo Segura-Cabrera Laboratorio de Bioinformática Centro de Biotecnología Genómica Instituto Politécnico Nacional Blvd. Del Maestro esquina Elías Piña, 88710 Reynosa, Tamaulipas, México. (899)9243627 ext. 87729 e-mail: asegurac@ipn.mx; aldosegura@gmail.com =========================================
Thank you for the information. When searching through the ZINC database, is it possible to exclude molecules containing certain functional groups, such as an amino group? Nancy On Fri, May 25, 2012 at 6:24 PM, Aldo Segura <aldosegura@gmail.com> wrote:
Dear Nancy,
I don't know how Pubchem works but I think that you should try to use ZINC database (zinc.docking.org) which has implemented a large number of filters (pH, toxic functional groups, etc) and the selected compounds can be downloaded as a compound library.
Best regards,
Aldo -- ========================================= Aldo Segura-Cabrera Laboratorio de Bioinformática Centro de Biotecnología Genómica Instituto Politécnico Nacional Blvd. Del Maestro esquina Elías Piña, 88710 Reynosa, Tamaulipas, México. (899)9243627 ext. 87729 e-mail: asegurac@ipn.mx; aldosegura@gmail.com =========================================
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