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Associating Drugs, Targets and Clinical Outcomes into an Integrated Network Affords a New Platform for Computer-Aided Drug Repurposing.

Oprea TI, Nielsen SK, Ursu O, Yang JJ, Taboureau O, Mathias SL, Kouskoumvekaki L, Sklar LA, Bologa CG.

Mol Inform. 2011 Mar 14;30(2-3):100-111.


Chemical informatics and target identification in a zebrafish phenotypic screen.

Laggner C, Kokel D, Setola V, Tolia A, Lin H, Irwin JJ, Keiser MJ, Cheung CY, Minor DL Jr, Roth BL, Peterson RT, Shoichet BK.

Nat Chem Biol. 2011 Dec 18;8(2):144-6. doi: 10.1038/nchembio.732.


ChEMBL: a large-scale bioactivity database for drug discovery.

Gaulton A, Bellis LJ, Bento AP, Chambers J, Davies M, Hersey A, Light Y, McGlinchey S, Michalovich D, Al-Lazikani B, Overington JP.

Nucleic Acids Res. 2012 Jan;40(Database issue):D1100-7. doi: 10.1093/nar/gkr777. Epub 2011 Sep 23.


Detecting drug interactions from adverse-event reports: interaction between paroxetine and pravastatin increases blood glucose levels.

Tatonetti NP, Denny JC, Murphy SN, Fernald GH, Krishnan G, Castro V, Yue P, Tsao PS, Kohane I, Roden DM, Altman RB.

Clin Pharmacol Ther. 2011 Jul;90(1):133-42. doi: 10.1038/clpt.2011.83. Epub 2011 May 25. Erratum in: Clin Pharmacol Ther. 2011 Sep;90(3):480. Tsau, P S [corrected to Tsao, P S].


Trial watch: Phase II failures: 2008-2010.

Arrowsmith J.

Nat Rev Drug Discov. 2011 May;10(5):328-9. doi: 10.1038/nrd3439. No abstract available.


Building the process-drug-side effect network to discover the relationship between biological processes and side effects.

Lee S, Lee KH, Song M, Lee D.

BMC Bioinformatics. 2011 Mar 29;12 Suppl 2:S2. doi: 10.1186/1471-2105-12-S2-S2.


Trial watch: phase III and submission failures: 2007-2010.

Arrowsmith J.

Nat Rev Drug Discov. 2011 Feb;10(2):87. doi: 10.1038/nrd3375. No abstract available.


Protein binding specificity versus promiscuity.

Schreiber G, Keating AE.

Curr Opin Struct Biol. 2011 Feb;21(1):50-61. doi: 10.1016/ Epub 2010 Nov 9. Review.


Ongoing and future developments at the Universal Protein Resource.

UniProt Consortium.

Nucleic Acids Res. 2011 Jan;39(Database issue):D214-9. doi: 10.1093/nar/gkq1020. Epub 2010 Nov 4.


Selective COX-1 inhibition: A therapeutic target to be reconsidered.

Perrone MG, Scilimati A, Simone L, Vitale P.

Curr Med Chem. 2010;17(32):3769-805. Review.


Protein adducts as prospective biomarkers of nevirapine toxicity.

Antunes AM, Godinho AL, Martins IL, Oliveira MC, Gomes RA, Coelho AV, Beland FA, Marques MM.

Chem Res Toxicol. 2010 Nov 15;23(11):1714-25. doi: 10.1021/tx100186t. Epub 2010 Sep 1.


Kinase inhibition-related adverse events predicted from in vitro kinome and clinical trial data.

Yang X, Huang Y, Crowson M, Li J, Maitland ML, Lussier YA.

J Biomed Inform. 2010 Jun;43(3):376-84. doi: 10.1016/j.jbi.2010.04.006. Epub 2010 May 1.


Extended-connectivity fingerprints.

Rogers D, Hahn M.

J Chem Inf Model. 2010 May 24;50(5):742-54. doi: 10.1021/ci100050t.


Cytokine-associated drug toxicity in human hepatocytes is associated with signaling network dysregulation.

Cosgrove BD, Alexopoulos LG, Hang TC, Hendriks BS, Sorger PK, Griffith LG, Lauffenburger DA.

Mol Biosyst. 2010 Jul;6(7):1195-206. doi: 10.1039/b926287c. Epub 2010 Apr 1.


A side effect resource to capture phenotypic effects of drugs.

Kuhn M, Campillos M, Letunic I, Jensen LJ, Bork P.

Mol Syst Biol. 2010;6:343. doi: 10.1038/msb.2009.98. Epub 2010 Jan 19.


The use of computer models in pharmaceutical safety evaluation.

Boyer S.

Altern Lab Anim. 2009 Nov;37(5):467-75. Review.


Prediction of drug-related cardiac adverse effects in humans--A: creation of a database of effects and identification of factors affecting their occurrence.

Matthews EJ, Frid AA.

Regul Toxicol Pharmacol. 2010 Apr;56(3):247-75. doi: 10.1016/j.yrtph.2009.11.006. Epub 2009 Nov 22.


Predicting new molecular targets for known drugs.

Keiser MJ, Setola V, Irwin JJ, Laggner C, Abbas AI, Hufeisen SJ, Jensen NH, Kuijer MB, Matos RC, Tran TB, Whaley R, Glennon RA, Hert J, Thomas KL, Edwards DD, Shoichet BK, Roth BL.

Nature. 2009 Nov 12;462(7270):175-81. doi: 10.1038/nature08506. Epub 2009 Nov 1.


The topology of drug-target interaction networks: implicit dependence on drug properties and target families.

Mestres J, Gregori-Puigjané E, Valverde S, Solé RV.

Mol Biosyst. 2009 Sep;5(9):1051-7. doi: 10.1039/b905821b. Epub 2009 Jul 8.


SePreSA: a server for the prediction of populations susceptible to serious adverse drug reactions implementing the methodology of a chemical-protein interactome.

Yang L, Luo H, Chen J, Xing Q, He L.

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W406-12. doi: 10.1093/nar/gkp312. Epub 2009 May 5.

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