PubChem Publications

Citing the Resources

Please see the PubChem Data Usage and Citation Guidelines page for information about how to cite individual or multiple records from a PubChem database. If you are referencing the overall PubChem Substance, Compound, or BioAssay database, the following articles can be cited:

	PubChem Substance and PubChem Compound
		Bolton E, Wang Y, Thiessen PA, Bryant SH. PubChem: Integrated Platform of Small Molecules and Biological Activities. Chapter 12 IN Annual Reports in Computational Chemistry, Volume 4, American Chemical Society, Washington, DC, 2008 Apr.

	PubChem BioAssay
		Wang Y, Xiao J, Suzek TO, Zhang J, Wang J, Zhou Z, Han L, Karapetyan K, Dracheva S, Shoemaker BA, Bolton E, Gindulyte A, Bryant SH. PubChem's BioAssay Database. Nucleic Acids Res. 2012 Jan;40(1):D400-12. (Epub 2011 Dec 2) doi:10.1093/nar/gkr1132. [PubMed PMID: 22140110] [Free Full Text at Oxford Journals]

Additional Journal Articles About PubChem

VIEW ALL PUBCHEM ARTICLES IN PUBMED >>

		Kim S, Bolton EE, Bryant SH. PubChem3D: conformer ensemble accuracy. J Cheminform. 2013 Jan 7;5(1):1. [Epub ahead of print] doi:10.1186/1758-2946-5-1. [PubMed PMID: 23289532] [Free Full Text on J Cheminform]
		Kim S, Bolton EE, Bryant SH. Effects of multiple conformers per compound upon 3-D similarity search and bioassay data analysis. J Cheminform 2012 Nov 7;4(1):28. doi:10.1186/1758-2946-4-28. [PubMed PMID: 23134593] [Free Full Text on J Cheminform]
		Zhang JD, Geer LY, Bolton EE, Bryant SH. Automated annotation of chemical names in the literature with tunable accuracy. J Cheminform. 2011 Nov 22;3(1):52. Epub ahead of print. doi:10.1186/1758-2946-3-52. [PubMed PMID: 22107874] [Free Full Text on J Cheminform]
		Bolton EE, Chen J, Kim S, Han L, He S, Shi W, Simonyan V, Sun Y, Thiessen PA, Wang J, Yu B, Zhang J, Bryant SH. PubChem3D: A new resource for scientists. J Cheminform. 2011 Sep 20;3(1):32. Epub ahead of print. doi:10.1186/1758-2946-3-32. [PubMed PMID: 21933373] [Free Full Text on J Cheminform] (Part of the PubChem3D thematic series with the (BMC) Journal of Cheminformatics: http://www.jcheminf.com/series/pubchem3d)
		Cheng T, Li Q, Wang Y, Bryant SH. Identifying compound-target associations by combining bioactivity profile similarity search and public databases mining. J Chem Inf Model. 2011 Sep 26;51(9):2440-8. Epub 2011 Aug 18. doi:10.1021/ci200192v. [PubMed PMID: 21834535] [Free Full Text on J Chem Inf Model]
		Zhou Z, Wang Y, Bryant SH. Multi-conformation 3D QSAR study of benzenesulfonyl-pyrazol-ester compounds and their analogs as cathepsin B inhibitors. J Mol Graph Model. 2011 Sep;30:135-47. Epub 2011 Jul 7. doi:10.1016/j.jmgm.2011.06.013. [PubMed PMID: 21798778]
		Kim S, Bolton EE, Bryant SH. PubChem3D: Biologically relevant 3-D similarity. J Cheminform. 2011 Jul 22;3(1):26. doi:10.1186/1758-2946-3-26. [PubMed PMID: 21781288] [Free Full Text on J Cheminform] (Part of the PubChem3D thematic series with the (BMC) Journal of Cheminformatics: http://www.jcheminf.com/series/pubchem3d)
		Kim S, Bolton EE, Bryant SH. PubChem3D: Shape compatibility filtering using molecular shape quadrupoles. J Cheminform. 2011 Jul 20;3(1):25. doi:10.1186/1758-2946-3-25. [PubMed PMID: 21774809] [Free Full Text on J Cheminform] (Part of the PubChem3D thematic series with the (BMC) Journal of Cheminformatics: http://www.jcheminf.com/series/pubchem3d)
		Bolton EE, Kim S, Bryant SH. PubChem3D: Similar conformers. J Cheminform. 2011 May 9;3(1):13. doi:10.1186/1758-2946-3-13. [PubMed PMID: 21554721] [Free Full Text on J Cheminform] (Part of the PubChem3D thematic series with the (BMC) Journal of Cheminformatics: http://www.jcheminf.com/series/pubchem3d)
		Bolton EE, Kim S, Bryant SH. PubChem3D: Diversity of shape. J Cheminform. 2011 Mar 21;3(1):9. doi:10.1186/1758-2946-3-9. [PubMed PMID: 21418625] [Free Full Text on J Cheminform] (Part of the PubChem3D thematic series with the (BMC) Journal of Cheminformatics: http://www.jcheminf.com/series/pubchem3d)
		Bolton EE, Kim S, Bryant SH. PubChem3D: Conformer generation. J Cheminform. 2011 Jan 27;3(1):4. doi:10.1186/1758-2946-3-4. [PubMed PMID: 21272340] [Free Full Text on J Cheminform] (Part of the PubChem3D thematic series with the (BMC) Journal of Cheminformatics: http://www.jcheminf.com/series/pubchem3d)
		Cheng T, Li Q, Wang Y, Bryant SH. Binary Classification of Aqueous Solubility Using Support Vector Machines with Reduction and Recombination Feature Selection. J Chem Inf Model. 2011 Jan 7. doi:10.1021/ci100364a. [Epub ahead of print]. [PubMed PMID: 21214224]
		Han L, Suzek TO, Wang Y, Bryant SH. The Text-mining based PubChem Bioassay neighboring analysis. BMC Bioinformatics. 2010 Nov 8;11:549. doi:10.1186/1471-2105-11-549. [PubMed PMID: 21059237] [Free Full Text at BioMed Central]
		Li Q, Cheng T, Wang Y, Bryant SH. PubChem as a public resource for drug discovery. Drug Discov Today. 2010 Dec;15(23-24):1052-7. Epub 2010 Oct 21. doi:10.1016/j.drudis.2010.10.003. [PubMed PMID: 20970519]
		Cheng T, Wang Y, Bryant SH. Investigating the correlations among the chemical structures, bioactivity profiles and molecular targets of small molecules. Bioinformatics. 2010 Nov 15;26(22):2881-8. Epub 2010 Oct 13. doi:10.1093/bioinformatics/btq550. [PubMed PMID: 20947527] [Free Full Text at Oxford Journals]
		Zhou Z, Wang Y, Bryant SH. QSAR models for predicting cathepsin B inhibition by small molecules--continuous and binary QSAR models to classify cathepsin B inhibition activities of small molecules. J Mol Graph Model. 2010 Jun;28(8):714-27. Epub 2010 Feb 1. doi:10.1016/j.jmgm.2010.01.009. [PubMed PMID: 20194042]
		Wang Y, Bolton E, Dracheva S, Karapetyan K, Shoemaker BA, Suzek TO, Wang J, Xiao J, Zhang J, Bryant SH. An overview of the PubChem BioAssay resource. Nucleic Acids Res. 2010 Jan;38(Database issue):D255-66. Epub 2009 Nov 19. doi:10.1093/nar/gkp965. [PubMed PMID: 19933261] [Free Full Text at Oxford Journals]
		Ihlenfeldt WD, Bolton EE, Bryant SH. The PubChem chemical structure sketcher. J Cheminform. 2009 Dec 17;1(1):20. doi:10.1186/1758-2946-1-20. [PubMed PMID: 20298522] [Free Full Text on J Cheminform]
		Li Q, Wang Y, Bryant SH. A novel method for mining highly imbalanced high-throughput screening data in PubChem. Bioinformatics. 2009 Dec 15;25(24):3310-6. Epub 2009 Oct 13. doi:10.1093/bioinformatics/btp589. [PubMed PMID: 19825798] [Free Full Text at Oxford Journals]
		Han L, Wang Y, Bryant SH. A survey of across-target bioactivity results of small molecules in PubChem. Bioinformatics. 2009 Sep 1;25(17):2251-5. Epub 2009 Jun 23. doi:10.1093/bioinformatics/btp380. [PubMed PMID: 19549631] [Free Full Text at Oxford Journals]
		Wang Y, Xiao J, Suzek TO, Zhang J, Wang J, Bryant SH. PubChem: a public information system for analyzing bioactivities of small molecules. Nucleic Acids Res. 2009 Jul 1;37(Web Server issue):W623-33. Epub 2009 Jun 4. doi:10.1093/nar/gkp456. [PubMed PMID: 19498078] [Free Full Text at Oxford Journals]
		Zhou Z, Wang Y, Bryant SH. Computational analysis of the cathepsin B inhibitors activities through LR-MMPBSA binding affinity calculation based on docked complex. J Comput Chem. 2009 Nov 15;30(14):2165-75. doi:10.1002/jcc.21214. [PubMed PMID: 19242965]
		Han L, Wang Y, Bryant SH. Developing and validating predictive decision tree models from mining chemical structural fingerprints and high-throughput screening data in PubChem. BMC Bioinformatics. 2008 Sep 25;9:401. doi:10.1186/1471-2105-9-401. [PubMed PMID: 18817552] [Free Full Text at BioMed Central]
		Fontaine F, Bolton E, Borodina Y, Bryant SH. Fast 3D shape screening of large chemical databases through alignment-recycling. Chem Cent J. 2007 Jun 6;1:12. doi:10.1186/1752-153X-1-12. [PubMed PMID: 17880744] [Free Full Text at Chemistry Central Journal]
		Borodina YV, Bolton E, Fontaine F, Bryant SH. Assessment of conformational ensemble sizes necessary for specific resolutions of coverage of conformational space. J Chem Inf Model. 2007 Jul-Aug;47(4):1428-37. Epub 2007 Jun 15. doi:10.1021/ci7000956. [PubMed PMID: 17569521]

Revised 16 January 2013