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
  Kim S, Thiessen PA, Bolton EE, Chen J, Fu G, Gindulyte A, Han L, He J, He S, Shoemaker BA, Wang J, Yu B, Zhang J, Bryant SH. PubChem Substance and Compound databases. Nucleic Acids Res. 2016 Jan 4; 44(D1):D1202-13. Epub 2015 Sep 22 [PubMed PMID: 26400175] doi: 10.1093/nar/gkv951 [Free Full Text at Oxford Journals]  
   
  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. Epub 2013 Nov 5 [PubMed PMID: 24198245] doi:10.1093/nar/gkt978. [Free Full Text at Oxford Journals]  
   
  
 
 
Additional Journal Articles About PubChem
 
 
  Kim S, Bolton EE, Bryant SH. Similar compounds versus similar conformers: complementarity between PubChem 2-D and 3-D neighboring sets. J Cheminform 2016 Nov 4;8:62. doi:10.1186/s13321-016-0163-1. [PubMed PMID: 27872662] [Free Full Text on J Cheminform]  Click here to read
  Kim S. Getting the most out of PubChem for virtual screening. Expert Opin Drug Discov. 2016 Aug 5; 11(9):843-55. doi: 10.1080/17460441.2016.1216967. Epub 2016 July 25. [PubMed PMID: 27454129] [Full Text]  
  Kim S, Thiessen PA, Cheng T, Yu B, Shoemaker BA, Wang J, Bolton EE, Wang Y, Bryant SH. Literature information in PubChem: associations between PubChem records and scientific articles. J Cheminform 2016 Jun 10;8:32. doi: 10.1186/s13321-016-0142-6. eCollection 2016. [PubMed PMID: 27293485] [Free Full Text on J Cheminform]  Click here to read
  Fu G, Ding Y, Seal A, Chen B, Sun Y, Bolton E. Predicting drug target interactions using meta-path-based semantic network analysis. BMC Bioinformatics 2016 Apr 12;17(1):160. doi: 10.1186/s12859-016-1005-x. [PubMed PMID: 27071755] [Full Text]  Click here to read
  Takeda T, Wang Y, Bryant SH. Structural insights of a PI3K/mTOR dual inhibitor with the morpholino-triazine scaffold. J Comput Aided Mol Des. 2016 Mar 8 [Epub ahead of print] doi:DOI 10.1007/s10822-016-9905-4. [PubMed PMID: 26956874] [Full Text]  
  Hao M, Wang Y, Bryant SH. Improved prediction of drug-target interactions using regularized least squares integrating with kernel fusion technique. Anal Chim Acta 2016 Feb 25;909:41-50. doi: 10.1016/j.aca.2016.01.014. Epub 2016 Jan 14. [PubMed PMID: 26851083]  Click here to read
  Kim S, McEwen LR, Stuart RB, Thiessen PA, Gindulyte A, Zhang J, Bolton EE, Bryant SH. PubChem Laboratory Safety Summary. ConfChem Newsletter, American Chemical Society Division of Chemical Education, Fall 2015 (November 5, 2015). [Full text: PubChem FTP]  
  Yu X, Geer LY, Han L, Bryant SH. Target enhanced 2D similarity search by using explicit biological activity annotations and profiles. J Cheminform 2015 Nov 17;7:55. doi: 10.1186/s13321-015-0103-5. eCollection 2015. [PubMed PMID: 26583046] [Free Full Text on J Cheminform] Click here to read
  Hähnke VD, Bolton EE, Bryant SH. PubChem atom environments. J Cheminform 2015 Aug 19;7:41. doi: 10.1186/s13321-015-0076-4. eCollection 2015. [PubMed PMID: 26300985] [Free Full Text on J Cheminform] Click here to read
  Fu G, Batchelor C, Dumontier M, Hastings J, Willighagen E, Bolton E. PubChemRDF: towards the semantic annotation of PubChem compound and substance databases. J Cheminform 2015 July 14; 7:34. doi: 10.1186/s13321-015-0084-4. eCollection 2015. [PubMed PMID: 26175801] [Free Full Text on J Cheminform] Click here to read
  Kim S, Han L, Yu B, Hähnke VD, Bolton EE, Bryant SH. PubChem structure-activity relationship (SAR) clusters. J Cheminform 2015 Jul 7; 7:33. doi: 10.1186/s13321-015-0070-x. eCollection 2015. [PubMed PMID: 26150895] [Free Full Text on J Cheminform] Click here to read
  Kim S, Thiessen PA, Bolton EE, Bryant SH. PUG-SOAP and PUG-REST: web services for programmatic access to chemical information in PubChem. Nucleic Acids Res 2015 Jul 1;43(W1):W605-11. doi: 10.1093/nar/gkv396. Epub 2015 Apr 30 [PubMed PMID: 25934803] [Free Full Text at Oxford Journals] Click here to read
  Cheng T, Pan Y, Hao M, Wang Y, Bryant SH. PubChem applications in drug discovery: A bibliometric analysis. Drug Discov Today 2014 Nov;19(11):1751-6. doi: 10.1016/j.drudis.2014.08.008. Epub 2014 Aug 27. Review.[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 Feb 24;54(2):407-18. doi: 10.1021/ci4005354. Epub 2014 Feb 5. [PubMed PMID: 24460210] [Free Full Text at ACS Publications] Click here to read 
  Ming H, Tiejun C, Yanli W, Stephen BH. Web search and data mining of natural products and their bioactivities in PubChem. Sci China Chem 2013 Oct;56(10). doi: 10.1007/s11426-013-4910-0. [PubMed PMID: 24363665] [Free Author Manuscript in PubMedCentral]  
  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. Epub 2013 Nov 5 [PubMed PMID: 24198245] doi:10.1093/nar/gkt978. [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 Apr 22;53(4):938-47. doi: 10.1021/ci300625c. Epub 2013 Apr 4. [PubMed PMID: 23496085] [Free Full Text at ACS Publications] Click here to read
  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. doi: 10.1186/1758-2946-3-52. [PubMed PMID: 22107874] [Free Full Text on J Cheminform]
Click here to read
  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. 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)
Click here to read
  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 Feb 28;51(2):229-36. doi: 10.1021/ci100364a. Epub 2011 Jan 7. [PubMed PMID: 21214224] [Free full text at ACS Publications] 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
  Bolton E, Wang Y, Thiessen PA, Bryant SH. PubChem: Integrated Platform of Small Molecules and Biological Activities. Chapter 12 IN Wheeler RA and Spellmeyer DC, eds. Annual Reports in Computational Chemistry, Volume 4. Oxford, UK: Elsevier, 2008, pp. 217-241. doi:10.1016/S1574-1400(08)00012-1. 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 29 November 2016