PubChem Publications

Please see the PubChem 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 article can be cited:

 

Kim S, Chen J, Cheng T, Gindulyte A, He J, He S, Li Q, Shoemaker BA, Thiessen PA, Yu B, Zaslavsky L, Zhang J, Bolton EE. PubChem in 2021: new data content and improved web interfaces. Nucleic Acids Res. 2021 Jan 8; 49(D1):D1388–D1395. doi:10.1093/nar/gkaa971.
[PubMed PMID: 33151290] [PubMed Central PMCID: PMC7778930] [Free Full Text]

 

Additional Journal Articles About PubChem

2022

Kim S, Cheng T, He S, Thiessen PA, Li Q, Gindulyte A, Bolton EE. PubChem Protein, Gene, Pathway, and Taxonomy Data Collections: Bridging Biology and Chemistry through Target-Centric Views of PubChem Data. J Mol Biol. 2022 Feb 25:167514. doi:10.1016/j.jmb.2022.167514. Epub ahead of print. PMID: 35227770.
[PubMed PMID: 35227770] [Free Full Text]

 

Sayers EW, Bolton EE, Brister JR, Canese K, Chan J, Comeau DC, Connor R, Funk K, Kelly C, Kim S, Madej T, Marchler-Bauer A, Lanczycki C, Lathrop S, Lu Z, Thibaud-Nissen F, Murphy T, Phan L, Skripchenko Y, Tse T, Wang J, Williams R, Trawick BW, Pruitt KD, Sherry ST. Database Resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2022 Jan 7; 50(D1):D20-D26. doi:10.1093/nar/gkab1112.
[PubMed PMID: 34850941] [PubMed Central PMCID: PMC8728269] [Free Full Text]

 

[Free Full Text]

 

2021

Kim S. Exploring Chemical Information in PubChem. Curr. Protoc. 2021 Aug 9; 1(8):e217. doi:https://doi.org/10.1002/cpz1.217.
[PubMed PMID: 34370395] [PubMed Central PMCID: PMC8363119] [Free Full Text]

 

Zaslavsky L, Cheng T, Gindulyte A, He S, Kim S, Li Q, Thiessen P, Yu B, Bolton EE. Discovering and Summarizing Relationships Between Chemicals, Genes, Proteins, and Diseases in PubChem. Front. Res. Metr. Anal. 2021 July 12; 6:689059. doi:10.3389/frma.2021.689059.
[PubMed PMID: 34322655] [PubMed Central PMCID: PMC8311438] [Free Full Text]

 

Elmassry MM, Kim S, Busby B. Predicting drug-metagenome interactions: Variation in the microbial β-glucuronidase level in the human gut metagenomes. PLoS ONE. 2021 Jan 7; 16(1):e0244876. doi:10.1371/journal.pone.0244876.
[PubMed PMID: 33411719] [PubMed Central PMCID: PMC7790408] [Free Full Text]

 

Kim S, Bucholtz EC, Briney K, Cornell AP, Cuadros J, Fulfer KD, Gupta T, Hepler-Smith E, Johnston DH, Lang ASID, Larsen D, Li Y, McEwen LR, Morsch LA, Muzyka JL, Belford RE. Teaching Cheminformatics through a Collaborative Intercollegiate Online Chemistry Course (OLCC). J. Chem. Educ. 2021 Feb 9; 98(2):416-425. doi:10.1021/acs.jchemed.0c01035.
[PubMed PMID: 33762777] [PubMed Central PMCID: PMC7976600] [Free Full Text]

 

Sayers EW, Beck J, Bolton EE, Bourexis D, Brister JR, Canese K, Comeau DC, Funk K, Kim S, Klimke W, Marchler-Bauer A, Landrum M, Lathrop S, Lu Z, Madden TL, O'Leary N, Phan L, Rangwala SH, Schneider VA, Skripchenko Y, Wang J, Ye J, Trawick BW, Pruitt KD, Sherry ST. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2021 Jan 8; 49(D1):D10-D17. doi:10.1093/nar/gkaa892.
[PubMed PMID: 33095870] [PubMed Central PMCID: PMC7778943] [Free Full Text]

 

2020

Kim S, Gindulyte A, Zhang J, Thiessen PA, Bolton EE. PubChem Periodic Table and Element pages: improving access to information on chemical elements from authoritative sources. Chemistry Teacher International. 2021 Mar 1; 3(1):57-65. doi:10.1515/cti-2020-0006.
[PubMed PMID: 34268481] [PubMed Central PMCID: PMC8276875] [Free Full Text]

 

Sayers EW, Beck J, Brister JR, Bolton EE, Canese K, Comeau DC, Funk K, Ketter A, Kim S, Kimchi A, Kitts PA, Kuznetsov A, Lathrop S, Lu Z, McGarvey K, Madden TL, Murphy TD, O'Leary N, Phan L, Schneider VA, Thibaud-Nissen F, Trawick BW, Pruitt KD, Ostell J. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2020 Jan 8; 48(D1):D9-D16. doi:10.1093/nar/gkz899.
[PubMed PMID: 31602479] [PubMed Central PMCID: PMC6943063] [Free Full Text]

 

2019

Kim S, Thiessen PA, Cheng T, Zhang J, Gindulyte A, Bolton EE. PUG-View: programmatic access to chemical annotations integrated in PubChem. J Cheminform. 2019 Aug 9; 11:56. doi:10.1186/s13321-019-0375-2.
[PubMed PMID: 31399858] [PubMed Central PMCID: PMC6688265] [Free Full Text]

 

Kim S, Gindulyte A, Zhang J, Thiessen PA, Bolton EE. PubChem Periodic Table and Element Pages. ConfChem Newsletter. Spring 2019. American Chemical Society Division of Chemical Education (2019 May 27).
[Free Full Text]

 

Kim S, Chen J, Cheng T, Gindulyte A, He J, He S, Li Q, Shoemaker BA, Thiessen PA, Yu B, Zaslavsky L, Zhang J, Bolton EE. PubChem 2019 update: improved access to chemical data. Nucleic Acids Res. 2019 Jan 8; 47(D1):D1102-D1109. doi:10.1093/nar/gky1033.
[PubMed PMID: 30371825] [PubMed Central PMCID: PMC6324075] [Free Full Text]

 

Sayers EW, Agarwala R, Bolton EE, Brister JR, Canese K, Clark K, Connor R, Fiorini N, Funk K, Hefferon T, Holmes JB, Kim S, Kimchi A, Kitts PA, Lathrop S, Lu Z, Madden TL, Marchler-Bauer A, Phan L, Schneider VA, Schoch CL, Pruitt KD, Ostell J. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2019 Jan 8; 47(D1):D23-D28. doi:10.1093/nar/gky1069.
[PubMed PMID: 30395293] [PubMed Central PMCID: PMC6323993] [Free Full Text]

 

2018

Kim S, Thiessen PA, Bolton EE. Programmatic Retrieval of Small Molecule Information from PubChem Using PUG-REST. In Kutchukian PS, ed. Chemical Biology Informatics and Modeling. Methods in Pharmacology and Toxicology. New York, NY: Humana Press, 2018, pp. 1-24. doi:10.1007/7653_2018_30.
[Full Text]

 

Kim S. Public Chemical Databases. In Ranganathan S, Nakai K, Schönbach C, and Gribskov M, eds. Encyclopedia of Bioinformatics and Computational Biology, vol. 2. Oxford, UK: Elsevier. 2019, pp. 628-639. doi:10.1016/B978-0-12-809633-8.20192-1.
[Full Text]

 

Kim S, Shoemaker BA, Bolton EE, Bryant SH. Finding Potential Multi-Target Ligands using PubChem. In Brown JB, ed. Computational Chemogenomics. Methods in Molecular Biology, vol. 1825. New York, NY: Humana Press, 2018, pp. 63-91. doi: 10.1007/978-1-4939-8639-2_2.
[Full Text]

 

Hähnke VD, Kim S, Bolton EE. PubChem chemical structure standardization. J Cheminform. 2018 Aug 10; 10:36. doi:10.1186/s13321-018-0293-8.
[PubMed PMID: 30097821] [PubMed Central PMCID: PMC6086778] [Free Full Text]

 

Kim S, Thiessen PA, Cheng T, Yu B, Bolton EE. An update on PUG-REST: RESTful interface for programmatic access to PubChem. Nucleic Acids Res. 2018 July 2; 46(W1):W563-570. doi:10.1093/nar/gky294.
[PubMed PMID: 29718389] [PubMed Central ID: PMC6030920] [Free Full Text]

 

2017

Cheng T, Hao M, Takeda T, Bryant SH, Wang Y. Large-Scale Prediction of Drug-Target Interaction: a Data-Centric Review. AAPS J. 2017 Jun 2; 19(5):1264-1275. doi:10.1208/s12248-017-0092-6.
[PubMed PMID: 28577120] [Free Full Text]

 

Wang Y, Cheng T, Bryant SH. PubChem BioAssay: A Decade's Development toward Open High-Throughput Screening Data Sharing. SLAS Discov. 2017 Jul 1; 22(6):655-666. doi: 10.1177/2472555216685069.
[PubMed PMID: 28346087] [PubMed Central PMCID: PMC5480605] [Free Full Text]

 

Butkiewicz M, Wang Y, Bryant SH, Lowe EW Jr, Weaver DC, Meiler J. High-Throughput Screening Assay Datasets from the PubChem Database. Chem Inform. 2017 April 26; 3(1):1.
[PubMed PMID: 29795804] [PubMed Central PMCID: PMC5962024] [Free Full Text]

 

Takeda T, Hao M, Cheng T, Bryant SH, Wang Y. Predicting drug-drug interactions through drug structural similarities and interaction networks incorporating pharmacokinetics and pharmacodynamics knowledge. J Cheminform. 2017 Mar 7; 9:16. doi: 10.1186/s13321-017-0200-8.
[PubMed PMID: 28316654] [PubMed Central PMCID: PMC5340788] [Free Full Text]

 

Hao M, Bryant SH, Wang Y. Predicting drug-target interactions by dual-network integrated logistic matrix factorization. Sci Rep. 2017 Jan 12; 7:40376. doi: 10.1038/srep40376.
[PubMed PMID: 28079135] [PubMed Central PMCID: PMC5227688] [Free Full Text]

 

Wang Y, Bryant SH, Cheng T, Wang J, Gindulyte A, Shoemaker BA, Thiessen PA, He S, Zhang J. PubChem BioAssay: 2017 update. Nucleic Acids Res. 2017 Jan 4; 45(D1):D955-D963. doi: 10.1093/nar/gkw1118.
[PubMed PMID: 27899599] [PubMed Central PMCID: PMC5210581] [Free Full Text]

 

2016

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] [PubMed Central PMCID: PMC5097428] [Free Full Text]
(Part of the PubChem3D Thematic Series with the Journal of Cheminformatics)

 

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.
[PubMed PMID: 27454129] [PubMed Central PMCID: PMC5045798] [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.
[PubMed PMID: 27293485] [PubMed Central PMCID: PMC4901473] [Free Full Text]

 

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] [PubMed Central PMCID: PMC4830032] [Free Full Text]

 

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 Apr; 30(4):323-30. doi: 10.1007/s10822-016-9905-4.
[PubMed PMID: 26956874] [PubMed Central PMCID: PMC4833818] [Free 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.
[PubMed PMID: 26851083] [PubMed Central PMCID: PMC474462] [Full Text]

 

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–D1213. doi:10.1093/nar/gkv951.
[PubMed PMID: 26400175] [PubMed Central PMCID: PMC4702940] [Free Full Text]

 

2015

Fu G, Bolton E, Rosinach NQ, Furlong LI, Nguyen V, Sheth AP, Bodenreider O, Dumontier M. Exposing provenance metadata using different RDF models. Proceedings of the International Conference on Semantic Web Applications and Tools for Life Sciences (SWAT4LS 2015) (2015 Dec 7-10).
[Free Full text] [arXiv:1509.02822]

 

Kim S, McEwen LR, Stuart RB, Thiessen PA, Gindulyte A, Zhang J, Bolton EE, Bryant SH. PubChem Laboratory Safety Summary. ConfChem Newsletter, Fall 2015. American Chemical Society Division of Chemical Education (2015 Nov 5).
[Free Full text]

 

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.
[PubMed PMID: 26583046] [PubMed Central PMCID: PMC4648974] [Free Full Text]

 

Hähnke VD, Bolton EE, Bryant SH. PubChem atom environments. J Cheminform. 2015 Aug 19; 7:41. doi: 10.1186/s13321-015-0076-4.
[PubMed PMID: 26300985] [PubMed Central PMCID: PMC4540750] [Free Full Text]

 

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.
[PubMed PMID: 26175801] [PubMed Central PMCID: PMC4500850] [Free Full Text]

 

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.
[PubMed PMID: 26150895] [PubMed Central PMCID: PMC4492103] [Free Full Text]
(Part of the PubChem3D Thematic Series with the Journal of Cheminformatics)

 

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-W611. doi: 10.1093/nar/gkv396.
[PubMed PMID: 25934803] [PubMed Central PMCID: PMC4489244] [Free Full Text]

 

Bolton E. Reporting biological assay screening results for maximum impact. Drug Discov Today Technol. 2015 Jul; 14:31-36. doi: 10.1016/j.ddtec.2015.03.004.
[PubMed PMID: 26194585] [PubMed Central PMCID: PMC4510462] [Full Text]

 

2014

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.
[PubMed PMID: 25168772] [PubMed Central PMCID: PMC4252728] [Full Text]

 

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.
[PubMed PMID: 24460210] [PubMed Central PMCID: PMC3956470] [Free Full Text]

 

2013

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):1424-1435. doi: 10.1007/s11426-013-4910-0.
[PubMed PMID: 24363665] [PubMed Central PMCID: PMC3869387] [Full Text]

 

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; 806:117-127. doi: 10.1016/j.aca.2013.10.050.
[PubMed PMID: 24331047] [PubMed Central PMCID: PMC3884825] [Full Text]

 

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-D1082. doi:10.1093/nar/gkt978.
[PubMed PMID: 24198245] [PubMed Central PMCID: PMC3965008] [Free Full Text]

 

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; 1:6. doi:10.7243/2050-2273-1-6.
[PubMed PMID: 23745168] [PubMed Central PMCID: PMC3671605] [Free Full Text]

 

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):938-947. doi: 10.1021/ci300625c.
[PubMed PMID: 23496085] [PubMed Central PMCID: PMC3633254] [Free Full Text]

 

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] [PubMed Central PMCID: PMC3547714] [Free Full Text]
(Part of the PubChem3D Thematic Series with the Journal of Cheminformatics)

 

2012

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] [PubMed Central PMCID: PMC3537644] [Free Full Text]
(Part of the PubChem3D Thematic Series with the Journal of Cheminformatics)

 

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 1;40(D1):D400-D412. doi:10.1093/nar/gkr1132.
[PubMed PMID: 22140110] [PubMed Central PMCID: PMC3245056] [Free Full Text]

 

2011

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] [PubMed Central PMCID: PMC3281788] [Free Full Text]

 

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] [PubMed Central PMCID: PMC3269824] [Free Full Text]
(Part of the PubChem3D Thematic Series with the Journal of Cheminformatics)

 

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. doi: 10.1021/ci200192v.
[PubMed PMID: 21834535] [PubMed Central PMCID: PMC3180241] [Free Full Text]

 

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; 30:135-147. doi: 10.1016/j.jmgm.2011.06.013.
[PubMed PMID: 21798778] [PubMed Central PMCID: PMC3167229] [Full Text]

 

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] [PubMed Central PMCID: PMC3223603] [Free Full Text]
(Part of the PubChem3D Thematic Series with the Journal of Cheminformatics)

 

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] [PubMed Central PMCID: PMC3158422] [Free Full Text]
(Part of the PubChem3D Thematic Series with the Journal of Cheminformatics)

 

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] [PubMed Central PMCID: PMC3120778] [Free Full Text]
(Part of the PubChem3D Thematic Series with the Journal of Cheminformatics)

 

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] [PubMed Central PMCID: PMC3072936] [Free Full Text]
(Part of the PubChem3D Thematic Series with the Journal of Cheminformatics)

 

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] [PubMed Central PMCID: PMC3042967] [Free Full Text]
(Part of the PubChem3D Thematic Series with the Journal of Cheminformatics)

 

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.
[PubMed PMID: 21214224] [PubMed Central PMCID: PMC3047290] [Free Full Text]

 

2010 and earlier

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] [PubMed Central PMCID: PMC3098095] [Free Full Text]

 

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. doi: 10.1016/j.drudis.2010.10.003.
[PubMed PMID: 20970519] [PubMed Central PMCID: PMC3010383] [Full Text]

 

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. doi: 10.1093/bioinformatics/btq550.
[PubMed PMID: 20947527] [PubMed Central PMCID: PMC2971579] [Free Full Text]

 

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. doi: 10.1016/j.jmgm.2010.01.009.
[PubMed PMID: 20194042] [PubMed Central PMCID: PMC2873115] [Full Text]

 

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. doi:10.1093/nar/gkp965.
[PubMed PMID: 19933261] [PubMed Central PMCID: PMC2808922] [Free Full Text]

 

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] [PubMed Central PMCID: PMC2820498] [Free Full Text]

 

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. doi: 10.1093/bioinformatics/btp589.
[PubMed PMID: 19825798] [PubMed Central PMCID: PMC2788930] [Free Full Text]

 

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. doi: 10.1093/bioinformatics/btp380.
[PubMed PMID: 19549631] [PubMed Central PMCID: PMC2734317] [Free Full Text]

 

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-W633. doi: 10.1093/nar/gkp456.
[PubMed PMID: 19498078] [PubMed Central PMCID: PMC2703903] [Free Full Text]

 

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] [PubMed Central PMCID: PMC2735608] [Full Text]

 

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] [PubMed Central PMCID: PMC2572623] [Free Full Text]

 

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.
[Full Text]

 

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] [PubMed Central PMCID: PMC1994057] [Free Full Text]

 

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. doi: 10.1021/ci7000956.
[PubMed PMID: 17569521] [PubMed Central PMCID: PMC2040338] [Full Text]

 

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