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, Elsevier: Oxford, UK; 2008, pp. 217-240. Click here to read
   
  PubChem BioAssay
  Wang Y, Suzek T, Zhang J, Wang J, He S, Cheng T, Shoemaker BA, Gindulyte A, Bryant SH. PubChem BioAssay: 2014 update. Nucleic Acids Res. 2014 Jan 1;42(1):D1075-82. doi:10.1093/nar/gkt978. Epub 2013 Nov 5 [PubMed PMID: 24198245] [Free Full Text at Oxford Journals]  
   
  
 
 
Additional Journal Articles About PubChem
 
 
  Cheng T, Pan Y, Hao M, Wang Y, Bryant SH. PubChem applications in drug discovery: A bibliometric analysis. Drug Discov Today 2014 Aug 25. pii: S1359-6446(14)00335-3. doi: 10.1016/j.drudis.2014.08.008. [Epub ahead of print][PubMed PMID: 25168772]  
  Pan Y, Cheng T, Wang Y, Bryant SH. Pathway Analysis for Drug Repositioning Based on Public Database Mining. J Chem Inf Model. 2014 Jan 26 (Epub ahead of print) doi: 10.1021/ci4005354 [PubMed PMID: 24460210] [Free Full Text at J Chem Inf Model]
  Hao M, Wang Y, Bryant SH. An efficient algorithm coupled with synthetic minority over-sampling technique to classify imbalanced PubChem BioAssay data. Anal Chim Acta 2014 Jan 2;806:117-27. doi: 10.1016/j.aca.2013.10.050. Epub 2013 Nov 6. [PubMed PMID: 24331047]
  Wang Y, Suzek T, Zhang J, Wang J, He S, Cheng T, Shoemaker BA, Gindulyte A, Bryant SH. PubChem BioAssay: 2014 update. Nucleic Acids Res. 2014 Jan 1;42(1):D1075-82. doi:10.1093/nar/gkt978. Epub 2013 Nov 5 [PubMed PMID: 24198245] [Free Full Text at Oxford Journals]  
  Li Q, Cheng T, Wang Y, Bryant SH. Characterizing protein domain associations by Small-molecule ligand binding. J Proteome Sci Comput Biol 2012 Dec 3;1. pii: 6. doi:10.7243/2050-2273-1-6. [PubMed PMID: 23745168] Click here to read
  Pan Y, Wang Y, Bryant SH. Pharmacophore and 3D-QSAR Characterization of 6-arylquinazolin-4-amines as Cdc2-like kinase 4 (Clk4) and Dual Specificity Tyrosine-phosphorylation-regulated Kinase 1A (Dyrk1A) inhibitors. J Chem Inf Model. 2013 Mar 16 [Epub ahead of print] doi:10.1021/ci300625c. [PubMed PMID: 23496085]
  Kim S, Bolton EE, Bryant SH. PubChem3D: conformer ensemble accuracy. J Cheminform. 2013 Jan 7;5(1):1. doi:10.1186/1758-2946-5-1. [PubMed PMID: 23289532] [Free Full Text on J Cheminform] Click here to read
  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]  
  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. doi:10.1093/nar/gkr1132. Epub 2011 Dec 2 [PubMed PMID: 22140110] [Free Full Text at Oxford Journals]  
  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] Click here to read
  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)
Click here to read
  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)
Click here to read
  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)
Click here to read
  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)
Click here to read
  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)
Click here to read
  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] Click here to read
  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] Click here to read
  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] Click here to read
  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] Click here to read
  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] Click here to read
  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] Click here to read
  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] Click here to read
  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] Click here to read
  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] Click here to read
  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] Click here to read
  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] Click here to read
  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] Click here to read
  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] Click here to read
  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] Click here to read
 
 
 Revised 04 September 2014