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Items: 1 to 50 of 198

1.

ROBOKOP: An Abstraction Layer and User Interface for Knowledge Graphs to Support Question Answering.

Morton K, Wang P, Bizon C, Cox S, Balhoff J, Kebede Y, Fecho K, Tropsha A.

Bioinformatics. 2019 Aug 13. pii: btz604. doi: 10.1093/bioinformatics/btz604. [Epub ahead of print]

PMID:
31410449
2.

Cheminformatics-driven discovery of polymeric micelle formulations for poorly soluble drugs.

Alves VM, Hwang D, Muratov E, Sokolsky-Papkov M, Varlamova E, Vinod N, Lim C, Andrade CH, Tropsha A, Kabanov A.

Sci Adv. 2019 Jun 26;5(6):eaav9784. doi: 10.1126/sciadv.aav9784. eCollection 2019 Jun.

3.

A novel approach for exposing and sharing clinical data: the Translator Integrated Clinical and Environmental Exposures Service.

Fecho K, Pfaff E, Xu H, Champion J, Cox S, Stillwell L, Peden DB, Bizon C, Krishnamurthy A, Tropsha A, Ahalt SC.

J Am Med Inform Assoc. 2019 Apr 26. pii: ocz042. doi: 10.1093/jamia/ocz042. [Epub ahead of print]

PMID:
31077269
4.

Materials Informatics.

Senderowitz H, Tropsha A.

J Chem Inf Model. 2018 Dec 24;58(12):2377-2379. doi: 10.1021/acs.jcim.8b00927. No abstract available.

PMID:
30990041
5.

Inter-Modular Linkers play a crucial role in governing the biosynthesis of non-ribosomal peptides.

Farag S, Bleich RM, Shank EA, Isayev O, Bowers AA, Tropsha A.

Bioinformatics. 2019 Feb 20. pii: btz127. doi: 10.1093/bioinformatics/btz127. [Epub ahead of print]

PMID:
30785185
6.

Quantitative Structure-Price Relationship (QS$R) Modeling and the Development of Economically Feasible Drug Discovery Projects.

Fernandez M, Ban F, Woo G, Isaev O, Perez C, Fokin V, Tropsha A, Cherkasov A.

J Chem Inf Model. 2019 Apr 22;59(4):1306-1313. doi: 10.1021/acs.jcim.8b00747. Epub 2019 Feb 28.

PMID:
30767528
7.

Oy Vey! A Comment on "Machine Learning of Toxicological Big Data Enables Read-Across Structure Activity Relationships Outperforming Animal Test Reproducibility".

Alves VM, Borba J, Capuzzi SJ, Muratov E, Andrade CH, Rusyn I, Tropsha A.

Toxicol Sci. 2019 Jan 1;167(1):3-4. doi: 10.1093/toxsci/kfy286. No abstract available.

PMID:
30500930
8.

Chemistry-Wide Association Studies (CWAS): A Novel Framework for Identifying and Interpreting Structure-Activity Relationships.

Low YS, Alves VM, Fourches D, Sedykh A, Andrade CH, Muratov EN, Rusyn I, Tropsha A.

J Chem Inf Model. 2018 Nov 26;58(11):2203-2213. doi: 10.1021/acs.jcim.8b00450. Epub 2018 Nov 9.

PMID:
30376324
9.

Deep reinforcement learning for de novo drug design.

Popova M, Isayev O, Tropsha A.

Sci Adv. 2018 Jul 25;4(7):eaap7885. doi: 10.1126/sciadv.aap7885. eCollection 2018 Jul.

10.

Chemistry, information and Frank: a tribute to Frank Brown.

Agrafiotis DK, Holloway MK, Johnson SA, Reynolds CH, Stouch TR, Tropsha A, Waller CL.

J Comput Aided Mol Des. 2018 Jul;32(7):723-729. doi: 10.1007/s10822-018-0135-9. Epub 2018 Jul 23. No abstract available.

PMID:
30039202
11.

Predicting Adverse Drug Effects from Literature- and Database-Mined Assertions.

La MK, Sedykh A, Fourches D, Muratov E, Tropsha A.

Drug Saf. 2018 Nov;41(11):1059-1072. doi: 10.1007/s40264-018-0688-5.

PMID:
29876834
12.

Conditional Toxicity Value (CTV) Predictor: An In Silico Approach for Generating Quantitative Risk Estimates for Chemicals.

Wignall JA, Muratov E, Sedykh A, Guyton KZ, Tropsha A, Rusyn I, Chiu WA.

Environ Health Perspect. 2018 May 29;126(5):057008. doi: 10.1289/EHP2998. eCollection 2018 May.

13.

Multi-Descriptor Read Across (MuDRA): A Simple and Transparent Approach for Developing Accurate Quantitative Structure-Activity Relationship Models.

Alves VM, Golbraikh A, Capuzzi SJ, Liu K, Lam WI, Korn DR, Pozefsky D, Andrade CH, Muratov EN, Tropsha A.

J Chem Inf Model. 2018 Jun 25;58(6):1214-1223. doi: 10.1021/acs.jcim.8b00124. Epub 2018 Jun 13.

PMID:
29809005
14.

Materials Informatics.

Senderowitz H, Tropsha A.

J Chem Inf Model. 2018 Jul 23;58(7):1313-1314. doi: 10.1021/acs.jcim.8b00016. Epub 2018 Apr 11. No abstract available.

PMID:
29638126
15.

Computer-Aided Discovery and Characterization of Novel Ebola Virus Inhibitors.

Capuzzi SJ, Sun W, Muratov EN, Martínez-Romero C, He S, Zhu W, Li H, Tawa G, Fisher EG, Xu M, Shinn P, Qiu X, García-Sastre A, Zheng W, Tropsha A.

J Med Chem. 2018 Apr 26;61(8):3582-3594. doi: 10.1021/acs.jmedchem.8b00035. Epub 2018 Apr 17.

16.

Quantitative high-throughput phenotypic screening of pediatric cancer cell lines identifies multiple opportunities for drug repurposing.

Shen M, Asawa R, Zhang YQ, Cunningham E, Sun H, Tropsha A, Janzen WP, Muratov EN, Capuzzi SJ, Farag S, Jadhav A, Blatt J, Simeonov A, Martinez NJ.

Oncotarget. 2017 Dec 19;9(4):4758-4772. doi: 10.18632/oncotarget.23462. eCollection 2018 Jan 12.

17.

A bibliometric review of drug repurposing.

Baker NC, Ekins S, Williams AJ, Tropsha A.

Drug Discov Today. 2018 Mar;23(3):661-672. doi: 10.1016/j.drudis.2018.01.018. Epub 2018 Jan 9. Review.

18.

Chemotext: A Publicly Available Web Server for Mining Drug-Target-Disease Relationships in PubMed.

Capuzzi SJ, Thornton TE, Liu K, Baker N, Lam WI, O'Banion CP, Muratov EN, Pozefsky D, Tropsha A.

J Chem Inf Model. 2018 Feb 26;58(2):212-218. doi: 10.1021/acs.jcim.7b00589. Epub 2018 Jan 19.

19.

Reproducibility, sharing and progress in nanomaterial databases.

Tropsha A, Mills KC, Hickey AJ.

Nat Nanotechnol. 2017 Dec 6;12(12):1111-1114. doi: 10.1038/nnano.2017.233. Review. No abstract available.

PMID:
29209007
20.

Modernization of Enoxaparin Molecular Weight Determination Using Homogeneous Standards.

Arnold KM, Capuzzi SJ, Xu Y, Muratov EN, Carrick K, Szajek AY, Tropsha A, Liu J.

Pharmaceuticals (Basel). 2017 Jul 22;10(3). pii: E66. doi: 10.3390/ph10030066.

21.

QSAR models of human data can enrich or replace LLNA testing for human skin sensitization.

Alves VM, Capuzzi SJ, Muratov E, Braga RC, Thornton T, Fourches D, Strickland J, Kleinstreuer N, Andrade CH, Tropsha A.

Green Chem. 2016 Dec 21;18(24):6501-6515. doi: 10.1039/C6GC01836J. Epub 2016 Oct 6.

22.

Universal fragment descriptors for predicting properties of inorganic crystals.

Isayev O, Oses C, Toher C, Gossett E, Curtarolo S, Tropsha A.

Nat Commun. 2017 Jun 5;8:15679. doi: 10.1038/ncomms15679.

23.

Alarms about structural alerts.

Alves V, Muratov E, Capuzzi S, Politi R, Low Y, Braga R, Zakharov AV, Sedykh A, Mokshyna E, Farag S, Andrade C, Kuz'min V, Fourches D, Tropsha A.

Green Chem. 2016 Aug 21;18(16):4348-4360. doi: 10.1039/C6GC01492E. Epub 2016 Jun 28.

24.

Computer-Assisted Decision Support for Student Admissions Based on Their Predicted Academic Performance.

Muratov E, Lewis M, Fourches D, Tropsha A, Cox WC.

Am J Pharm Educ. 2017 Apr;81(3):46. doi: 10.5688/ajpe81346.

25.

Chemical toxicity prediction for major classes of industrial chemicals: Is it possible to develop universal models covering cosmetics, drugs, and pesticides?

Alves VM, Muratov EN, Zakharov A, Muratov NN, Andrade CH, Tropsha A.

Food Chem Toxicol. 2018 Feb;112:526-534. doi: 10.1016/j.fct.2017.04.008. Epub 2017 Apr 12.

26.

New drug candidates for liposomal delivery identified by computer modeling of liposomes' remote loading and leakage.

Cern A, Marcus D, Tropsha A, Barenholz Y, Goldblum A.

J Control Release. 2017 Apr 28;252:18-27. doi: 10.1016/j.jconrel.2017.02.015. Epub 2017 Feb 16.

PMID:
28215669
27.

Phantom PAINS: Problems with the Utility of Alerts for Pan-Assay INterference CompoundS.

Capuzzi SJ, Muratov EN, Tropsha A.

J Chem Inf Model. 2017 Mar 27;57(3):417-427. doi: 10.1021/acs.jcim.6b00465. Epub 2017 Feb 25.

28.

Chembench: A Publicly Accessible, Integrated Cheminformatics Portal.

Capuzzi SJ, Kim IS, Lam WI, Thornton TE, Muratov EN, Pozefsky D, Tropsha A.

J Chem Inf Model. 2017 Feb 27;57(2):105-108. doi: 10.1021/acs.jcim.6b00462. Epub 2017 Jan 19.

29.

Public (Q)SAR Services, Integrated Modeling Environments, and Model Repositories on the Web: State of the Art and Perspectives for Future Development.

Tetko IV, Maran U, Tropsha A.

Mol Inform. 2017 Mar;36(3). doi: 10.1002/minf.201600082. Epub 2016 Oct 25. Review.

PMID:
27778468
30.

Comparative Analysis of QSAR-based vs. Chemical Similarity Based Predictors of GPCRs Binding Affinity.

Luo M, Wang XS, Tropsha A.

Mol Inform. 2016 Jan;35(1):36-41. doi: 10.1002/minf.201500038. Epub 2015 Oct 23.

PMID:
27491652
31.

Pred-hERG: A Novel web-Accessible Computational Tool for Predicting Cardiac Toxicity.

Braga RC, Alves VM, Silva MF, Muratov E, Fourches D, Lião LM, Tropsha A, Andrade CH.

Mol Inform. 2015 Oct;34(10):698-701. doi: 10.1002/minf.201500040. Epub 2015 Jul 20.

32.

Trust, but Verify II: A Practical Guide to Chemogenomics Data Curation.

Fourches D, Muratov E, Tropsha A.

J Chem Inf Model. 2016 Jul 25;56(7):1243-52. doi: 10.1021/acs.jcim.6b00129. Epub 2016 Jun 22. Review.

33.

Docking and Scoring with Target-Specific Pose Classifier Succeeds in Native-Like Pose Identification But Not Binding Affinity Prediction in the CSAR 2014 Benchmark Exercise.

Politi R, Convertino M, Popov K, Dokholyan NV, Tropsha A.

J Chem Inf Model. 2016 Jun 27;56(6):1032-41. doi: 10.1021/acs.jcim.5b00751. Epub 2016 Apr 20.

PMID:
27050767
34.

CERAPP: Collaborative Estrogen Receptor Activity Prediction Project.

Mansouri K, Abdelaziz A, Rybacka A, Roncaglioni A, Tropsha A, Varnek A, Zakharov A, Worth A, Richard AM, Grulke CM, Trisciuzzi D, Fourches D, Horvath D, Benfenati E, Muratov E, Wedebye EB, Grisoni F, Mangiatordi GF, Incisivo GM, Hong H, Ng HW, Tetko IV, Balabin I, Kancherla J, Shen J, Burton J, Nicklaus M, Cassotti M, Nikolov NG, Nicolotti O, Andersson PL, Zang Q, Politi R, Beger RD, Todeschini R, Huang R, Farag S, Rosenberg SA, Slavov S, Hu X, Judson RS.

Environ Health Perspect. 2016 Jul;124(7):1023-33. doi: 10.1289/ehp.1510267. Epub 2016 Feb 23.

35.

Computational Methods for Drug Discovery and Design.

Tropsha A, Bajorath J.

J Med Chem. 2016 Jan 14;59(1):1. doi: 10.1021/acs.jmedchem.5b01945. Epub 2015 Dec 30. No abstract available.

PMID:
26716466
36.

QSAR Modeling and Prediction of Drug-Drug Interactions.

Zakharov AV, Varlamova EV, Lagunin AA, Dmitriev AV, Muratov EN, Fourches D, Kuz'min VE, Poroikov VV, Tropsha A, Nicklaus MC.

Mol Pharm. 2016 Feb 1;13(2):545-56. doi: 10.1021/acs.molpharmaceut.5b00762. Epub 2016 Jan 5.

PMID:
26669717
37.

Computer-aided design of carbon nanotubes with the desired bioactivity and safety profiles.

Fourches D, Pu D, Li L, Zhou H, Mu Q, Su G, Yan B, Tropsha A.

Nanotoxicology. 2016;10(3):374-83. doi: 10.3109/17435390.2015.1073397. Epub 2015 Nov 2.

38.

Comprehensive characterization of the Published Kinase Inhibitor Set.

Elkins JM, Fedele V, Szklarz M, Abdul Azeez KR, Salah E, Mikolajczyk J, Romanov S, Sepetov N, Huang XP, Roth BL, Al Haj Zen A, Fourches D, Muratov E, Tropsha A, Morris J, Teicher BA, Kunkel M, Polley E, Lackey KE, Atkinson FL, Overington JP, Bamborough P, Müller S, Price DJ, Willson TM, Drewry DH, Knapp S, Zuercher WJ.

Nat Biotechnol. 2016 Jan;34(1):95-103. doi: 10.1038/nbt.3374. Epub 2015 Oct 26.

PMID:
26501955
39.

Cheminformatics-aided pharmacovigilance: application to Stevens-Johnson Syndrome.

Low YS, Caster O, Bergvall T, Fourches D, Zang X, Norén GN, Rusyn I, Edwards R, Tropsha A.

J Am Med Inform Assoc. 2016 Sep;23(5):968-78. doi: 10.1093/jamia/ocv127. Epub 2015 Oct 24.

40.

Curation of chemogenomics data.

Fourches D, Muratov E, Tropsha A.

Nat Chem Biol. 2015 Aug;11(8):535. doi: 10.1038/nchembio.1881. No abstract available.

PMID:
26196763
41.

Beware of R(2): Simple, Unambiguous Assessment of the Prediction Accuracy of QSAR and QSPR Models.

Alexander DL, Tropsha A, Winkler DA.

J Chem Inf Model. 2015 Jul 27;55(7):1316-22. doi: 10.1021/acs.jcim.5b00206. Epub 2015 Jul 9.

42.

Toxicokinetic Triage for Environmental Chemicals.

Wambaugh JF, Wetmore BA, Pearce R, Strope C, Goldsmith R, Sluka JP, Sedykh A, Tropsha A, Bosgra S, Shah I, Judson R, Thomas RS, Setzer RW.

Toxicol Sci. 2015 Sep;147(1):55-67. doi: 10.1093/toxsci/kfv118. Epub 2015 Jun 16.

43.

Letter from the editors.

Merz KM Jr, Rarey M, Tropsha A, Wahab HA.

J Chem Inf Model. 2015 Apr 27;55(4):719-20. doi: 10.1021/acs.jcim.5b00180. No abstract available.

PMID:
25912660
44.

Drug Side Effect Profiles as Molecular Descriptors for Predictive Modeling of Target Bioactivity.

Baker NC, Fourches D, Tropsha A.

Mol Inform. 2015 Feb;34(2-3):160-70. doi: 10.1002/minf.201400134. Epub 2015 Feb 20.

PMID:
27490038
45.

Predicting chemically-induced skin reactions. Part I: QSAR models of skin sensitization and their application to identify potentially hazardous compounds.

Alves VM, Muratov E, Fourches D, Strickland J, Kleinstreuer N, Andrade CH, Tropsha A.

Toxicol Appl Pharmacol. 2015 Apr 15;284(2):262-72. doi: 10.1016/j.taap.2014.12.014. Epub 2015 Jan 3.

46.

Predicting chemically-induced skin reactions. Part II: QSAR models of skin permeability and the relationships between skin permeability and skin sensitization.

Alves VM, Muratov E, Fourches D, Strickland J, Kleinstreuer N, Andrade CH, Tropsha A.

Toxicol Appl Pharmacol. 2015 Apr 15;284(2):273-80. doi: 10.1016/j.taap.2014.12.013. Epub 2015 Jan 3.

47.

Target-specific native/decoy pose classifier improves the accuracy of ligand ranking in the CSAR 2013 benchmark.

Fourches D, Politi R, Tropsha A.

J Chem Inf Model. 2015 Jan 26;55(1):63-71. doi: 10.1021/ci500519w. Epub 2014 Dec 18.

PMID:
25521713
48.

Clozapine-induced agranulocytosis is associated with rare HLA-DQB1 and HLA-B alleles.

Goldstein JI, Jarskog LF, Hilliard C, Alfirevic A, Duncan L, Fourches D, Huang H, Lek M, Neale BM, Ripke S, Shianna K, Szatkiewicz JP, Tropsha A, van den Oord EJ, Cascorbi I, Dettling M, Gazit E, Goff DC, Holden AL, Kelly DL, Malhotra AK, Nielsen J, Pirmohamed M, Rujescu D, Werge T, Levy DL, Josiassen RC, Kennedy JL, Lieberman JA, Daly MJ, Sullivan PF.

Nat Commun. 2014 Sep 4;5:4757. doi: 10.1038/ncomms5757.

49.

Expanding the scope of drug repurposing in pediatrics: the Children's Pharmacy Collaborative.

Blatt J, Farag S, Corey SJ, Sarrimanolis Z, Muratov E, Fourches D, Tropsha A, Janzen WP.

Drug Discov Today. 2014 Nov;19(11):1696-1698. doi: 10.1016/j.drudis.2014.08.003. Epub 2014 Aug 19.

50.

Prediction of binding affinity and efficacy of thyroid hormone receptor ligands using QSAR and structure-based modeling methods.

Politi R, Rusyn I, Tropsha A.

Toxicol Appl Pharmacol. 2014 Oct 1;280(1):177-89. doi: 10.1016/j.taap.2014.07.009. Epub 2014 Jul 21.

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