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Items: 1 to 50 of 254

1.

Ebola Virus Bayesian Machine Learning Models Enable New in Vitro Leads.

Anantpadma M, Lane T, Zorn KM, Lingerfelt MA, Clark AM, Freundlich JS, Davey RA, Madrid PB, Ekins S.

ACS Omega. 2019 Jan 31;4(1):2353-2361. doi: 10.1021/acsomega.8b02948. Epub 2019 Jan 30.

2.

Halogen Substitution Influences Ketamine Metabolism by Cytochrome P450 2B6: In Vitro and Computational Approaches.

Wang PF, Neiner A, Lane TR, Zorn KM, Ekins S, Kharasch ED.

Mol Pharm. 2019 Feb 4;16(2):898-906. doi: 10.1021/acs.molpharmaceut.8b01214. Epub 2019 Jan 10.

PMID:
30589555
3.

Synergistic Lethality of a Binary Inhibitor of Mycobacterium tuberculosis KasA.

Kumar P, Capodagli GC, Awasthi D, Shrestha R, Maharaja K, Sukheja P, Li SG, Inoyama D, Zimmerman M, Ho Liang HP, Sarathy J, Mina M, Rasic G, Russo R, Perryman AL, Richmann T, Gupta A, Singleton E, Verma S, Husain S, Soteropoulos P, Wang Z, Morris R, Porter G, Agnihotri G, Salgame P, Ekins S, Rhee KY, Connell N, Dartois V, Neiditch MB, Freundlich JS, Alland D.

MBio. 2018 Dec 18;9(6). pii: e02101-17. doi: 10.1128/mBio.02101-17.

4.

High Throughput and Computational Repurposing for Neglected Diseases.

Hernandez HW, Soeung M, Zorn KM, Ashoura N, Mottin M, Andrade CH, Caffrey CR, de Siqueira-Neto JL, Ekins S.

Pharm Res. 2018 Dec 17;36(2):27. doi: 10.1007/s11095-018-2558-3. Review.

PMID:
30560386
5.

A rapid method for estimation of the efficacy of potential antimicrobials in humans and animals by agar diffusion assay.

Salina EG, Ekins S, Makarov VA.

Chem Biol Drug Des. 2018 Nov 23. doi: 10.1111/cbdd.13427. [Epub ahead of print]

PMID:
30468306
6.

The EU approved antimalarial pyronaridine shows antitubercular activity and synergy with rifampicin, targeting RNA polymerase.

Mori G, Orena BS, Franch C, Mitchenall LA, Godbole AA, Rodrigues L, Aguilar-Pérez C, Zemanová J, Huszár S, Forbak M, Lane TR, Sabbah M, Deboosere N, Frita R, Vandeputte A, Hoffmann E, Russo R, Connell N, Veilleux C, Jha RK, Kumar P, Freundlich JS, Brodin P, Aínsa JA, Nagaraja V, Maxwell A, Mikušová K, Pasca MR, Ekins S.

Tuberculosis (Edinb). 2018 Sep;112:98-109. doi: 10.1016/j.tube.2018.08.004. Epub 2018 Aug 11.

PMID:
30205975
7.

Characterization of new, efficient Mycobacterium tuberculosis topoisomerase-I inhibitors and their interaction with human ABC multidrug transporters.

Temesszentandrási-Ambrus C, Tóth S, Verma R, Bánhegyi P, Szabadkai I, Baska F, Szántai-Kis C, Hartkoorn RC, Lingerfelt MA, Sarkadi B, Szakács G, Őrfi L, Nagaraja V, Ekins S, Telbisz Á.

PLoS One. 2018 Sep 5;13(9):e0202749. doi: 10.1371/journal.pone.0202749. eCollection 2018.

8.

Doing it All - How Families are Reshaping Rare Disease Research.

Ekins S, Perlstein EO.

Pharm Res. 2018 Aug 16;35(10):192. doi: 10.1007/s11095-018-2481-7.

PMID:
30116974
9.

Comparing Multiple Machine Learning Algorithms and Metrics for Estrogen Receptor Binding Prediction.

Russo DP, Zorn KM, Clark AM, Zhu H, Ekins S.

Mol Pharm. 2018 Oct 1;15(10):4361-4370. doi: 10.1021/acs.molpharmaceut.8b00546. Epub 2018 Aug 28.

PMID:
30114914
10.

Naïve Bayesian Models for Vero Cell Cytotoxicity.

Perryman AL, Patel JS, Russo R, Singleton E, Connell N, Ekins S, Freundlich JS.

Pharm Res. 2018 Jun 29;35(9):170. doi: 10.1007/s11095-018-2439-9.

PMID:
29959603
11.

The A-Z of Zika drug discovery.

Mottin M, Borba JVVB, Braga RC, Torres PHM, Martini MC, Proenca-Modena JL, Judice CC, Costa FTM, Ekins S, Perryman AL, Horta Andrade C.

Drug Discov Today. 2018 Nov;23(11):1833-1847. doi: 10.1016/j.drudis.2018.06.014. Epub 2018 Jun 20. Review.

PMID:
29935345
12.

Assessment of Substrate-Dependent Ligand Interactions at the Organic Cation Transporter OCT2 Using Six Model Substrates.

Sandoval PJ, Zorn KM, Clark AM, Ekins S, Wright SH.

Mol Pharmacol. 2018 Sep;94(3):1057-1068. doi: 10.1124/mol.117.111443. Epub 2018 Jun 8.

PMID:
29884691
13.

Comparing and Validating Machine Learning Models for Mycobacterium tuberculosis Drug Discovery.

Lane T, Russo DP, Zorn KM, Clark AM, Korotcov A, Tkachenko V, Reynolds RC, Perryman AL, Freundlich JS, Ekins S.

Mol Pharm. 2018 Oct 1;15(10):4346-4360. doi: 10.1021/acs.molpharmaceut.8b00083. Epub 2018 Apr 26.

PMID:
29672063
14.

Data Mining and Computational Modeling of High-Throughput Screening Datasets.

Ekins S, Clark AM, Dole K, Gregory K, Mcnutt AM, Spektor AC, Weatherall C, Litterman NK, Bunin BA.

Methods Mol Biol. 2018;1755:197-221. doi: 10.1007/978-1-4939-7724-6_14.

15.

A multitarget approach to drug discovery inhibiting Mycobacterium tuberculosis PyrG and PanK.

Chiarelli LR, Mori G, Orena BS, Esposito M, Lane T, de Jesus Lopes Ribeiro AL, Degiacomi G, Zemanová J, Szádocka S, Huszár S, Palčeková Z, Manfredi M, Gosetti F, Lelièvre J, Ballell L, Kazakova E, Makarov V, Marengo E, Mikusova K, Cole ST, Riccardi G, Ekins S, Pasca MR.

Sci Rep. 2018 Feb 16;8(1):3187. doi: 10.1038/s41598-018-21614-4.

16.

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.

PMID:
29330123
17.

Efficacy of Tilorone Dihydrochloride against Ebola Virus Infection.

Ekins S, Lingerfelt MA, Comer JE, Freiberg AN, Mirsalis JC, O'Loughlin K, Harutyunyan A, McFarlane C, Green CE, Madrid PB.

Antimicrob Agents Chemother. 2018 Jan 25;62(2). pii: e01711-17. doi: 10.1128/AAC.01711-17. Print 2018 Feb.

18.

Comparison of Deep Learning With Multiple Machine Learning Methods and Metrics Using Diverse Drug Discovery Data Sets.

Korotcov A, Tkachenko V, Russo DP, Ekins S.

Mol Pharm. 2017 Dec 4;14(12):4462-4475. doi: 10.1021/acs.molpharmaceut.7b00578. Epub 2017 Nov 13.

19.

Addressing the Metabolic Stability of Antituberculars through Machine Learning.

Stratton TP, Perryman AL, Vilchèze C, Russo R, Li SG, Patel JS, Singleton E, Ekins S, Connell N, Jacobs WR Jr, Freundlich JS.

ACS Med Chem Lett. 2017 Sep 14;8(10):1099-1104. doi: 10.1021/acsmedchemlett.7b00299. eCollection 2017 Oct 12.

20.

The new alchemy: Online networking, data sharing and research activity distribution tools for scientists.

Williams AJ, Peck L, Ekins S.

F1000Res. 2017 Aug 3;6:1315. doi: 10.12688/f1000research.12185.1. eCollection 2017.

21.

Ahead of Our Time: Collaboration in Modeling Then and Now.

Arnold RJG, Ekins S.

Pharmacoeconomics. 2017 Sep;35(9):975-976. doi: 10.1007/s40273-017-0532-2. No abstract available.

PMID:
28660474
22.

Rosuvastatin and Atorvastatin Are Ligands of the Human Constitutive Androstane Receptor/Retinoid X Receptor α Complex.

Režen T, Hafner M, Kortagere S, Ekins S, Hodnik V, Rozman D.

Drug Metab Dispos. 2017 Aug;45(8):974-976. doi: 10.1124/dmd.117.075523. Epub 2017 May 23.

PMID:
28536098
23.

A Phenotypic Based Target Screening Approach Delivers New Antitubercular CTP Synthetase Inhibitors.

Esposito M, Szadocka S, Degiacomi G, Orena BS, Mori G, Piano V, Boldrin F, Zemanová J, Huszár S, Barros D, Ekins S, Lelièvre J, Manganelli R, Mattevi A, Pasca MR, Riccardi G, Ballell L, Mikušová K, Chiarelli LR.

ACS Infect Dis. 2017 Jun 9;3(6):428-437. doi: 10.1021/acsinfecdis.7b00006. Epub 2017 May 11.

PMID:
28475832
24.

α7-Nicotinic acetylcholine receptor inhibition by indinavir: implications for cognitive dysfunction in treated HIV disease.

Ekins S, Mathews P, Saito EK, Diaz N, Naylor D, Chung J, McMurtray AM.

AIDS. 2017 May 15;31(8):1083-1089. doi: 10.1097/QAD.0000000000001488.

PMID:
28358738
25.

Molecular dynamics simulations of Zika virus NS3 helicase: Insights into RNA binding site activity.

Mottin M, Braga RC, da Silva RA, Silva JHMD, Perryman AL, Ekins S, Andrade CH.

Biochem Biophys Res Commun. 2017 Oct 28;492(4):643-651. doi: 10.1016/j.bbrc.2017.03.070. Epub 2017 Mar 21.

PMID:
28341122
26.

A summary of some EU funded Tuberculosis drug discovery collaborations.

Ekins S.

Drug Discov Today. 2017 Mar;22(3):479-480. doi: 10.1016/j.drudis.2017.03.002. No abstract available.

PMID:
28325272
27.

Machine learning and docking models for Mycobacterium tuberculosis topoisomerase I.

Ekins S, Godbole AA, Kéri G, Orfi L, Pato J, Bhat RS, Verma R, Bradley EK, Nagaraja V.

Tuberculosis (Edinb). 2017 Mar;103:52-60. doi: 10.1016/j.tube.2017.01.005. Epub 2017 Jan 20.

PMID:
28237034
28.

Industrializing rare disease therapy discovery and development.

Ekins S.

Nat Biotechnol. 2017 Feb 8;35(2):117-118. doi: 10.1038/nbt.3787. No abstract available.

29.

Collaborative drug discovery for More Medicines for Tuberculosis (MM4TB).

Ekins S, Spektor AC, Clark AM, Dole K, Bunin BA.

Drug Discov Today. 2017 Mar;22(3):555-565. doi: 10.1016/j.drudis.2016.10.009. Epub 2016 Nov 22. Review.

30.

Non-classical transpeptidases yield insight into new antibacterials.

Kumar P, Kaushik A, Lloyd EP, Li SG, Mattoo R, Ammerman NC, Bell DT, Perryman AL, Zandi TA, Ekins S, Ginell SL, Townsend CA, Freundlich JS, Lamichhane G.

Nat Chem Biol. 2017 Jan;13(1):54-61. doi: 10.1038/nchembio.2237. Epub 2016 Nov 7.

31.

Learning from the past for TB drug discovery in the future.

Mikušová K, Ekins S.

Drug Discov Today. 2017 Mar;22(3):534-545. doi: 10.1016/j.drudis.2016.09.025. Epub 2016 Oct 4. Review.

32.

OpenZika: An IBM World Community Grid Project to Accelerate Zika Virus Drug Discovery.

Ekins S, Perryman AL, Horta Andrade C.

PLoS Negl Trop Dis. 2016 Oct 20;10(10):e0005023. doi: 10.1371/journal.pntd.0005023. eCollection 2016 Oct.

33.

Illustrating and homology modeling the proteins of the Zika virus.

Ekins S, Liebler J, Neves BJ, Lewis WG, Coffee M, Bienstock R, Southan C, Andrade CH.

Version 2. F1000Res. 2016 Mar 3 [revised 2016 Jan 1];5:275. eCollection 2016.

34.

Raising awareness of the importance of funding for tuberculosis small-molecule research.

Riccardi G, Old IG, Ekins S.

Drug Discov Today. 2017 Mar;22(3):487-491. doi: 10.1016/j.drudis.2016.09.012. Epub 2016 Sep 21.

PMID:
27664546
35.

Enabling Anyone to Translate Clinically Relevant Ideas to Therapies.

Ekins S, Diaz N, Chung J, Mathews P, McMurtray A.

Pharm Res. 2017 Jan;34(1):1-6. doi: 10.1007/s11095-016-2039-5. Epub 2016 Sep 12.

PMID:
27620174
36.

The Next Era: Deep Learning in Pharmaceutical Research.

Ekins S.

Pharm Res. 2016 Nov;33(11):2594-603. doi: 10.1007/s11095-016-2029-7. Epub 2016 Sep 6. Review.

37.

Lack of Influence of Substrate on Ligand Interaction with the Human Multidrug and Toxin Extruder, MATE1.

Martínez-Guerrero LJ, Morales M, Ekins S, Wright SH.

Mol Pharmacol. 2016 Sep;90(3):254-64. doi: 10.1124/mol.116.105056. Epub 2016 Jul 14.

38.

Machine Learning Model Analysis and Data Visualization with Small Molecules Tested in a Mouse Model of Mycobacterium tuberculosis Infection (2014-2015).

Ekins S, Perryman AL, Clark AM, Reynolds RC, Freundlich JS.

J Chem Inf Model. 2016 Jul 25;56(7):1332-43. doi: 10.1021/acs.jcim.6b00004. Epub 2016 Jul 1.

39.

Predictive modeling targets thymidylate synthase ThyX in Mycobacterium tuberculosis.

Djaout K, Singh V, Boum Y, Katawera V, Becker HF, Bush NG, Hearnshaw SJ, Pritchard JE, Bourbon P, Madrid PB, Maxwell A, Mizrahi V, Myllykallio H, Ekins S.

Sci Rep. 2016 Jun 10;6:27792. doi: 10.1038/srep27792.

40.

Shedding Light on Synergistic Chemical Genetic Connections with Machine Learning.

Ekins S, Siqueira-Neto JL.

Cell Syst. 2015 Dec 23;1(6):377-9. doi: 10.1016/j.cels.2015.12.005. Epub 2015 Dec 23.

41.

Open drug discovery for the Zika virus.

Ekins S, Mietchen D, Coffee M, Stratton TP, Freundlich JS, Freitas-Junior L, Muratov E, Siqueira-Neto J, Williams AJ, Andrade C.

F1000Res. 2016 Feb 9;5:150. doi: 10.12688/f1000research.8013.1. eCollection 2016.

42.

Open Source Bayesian Models. 3. Composite Models for Prediction of Binned Responses.

Clark AM, Dole K, Ekins S.

J Chem Inf Model. 2016 Feb 22;56(2):275-85. doi: 10.1021/acs.jcim.5b00555. Epub 2016 Jan 19.

43.

Modeling error in experimental assays using the bootstrap principle: understanding discrepancies between assays using different dispensing technologies.

Hanson SM, Ekins S, Chodera JD.

J Comput Aided Mol Des. 2015 Dec;29(12):1073-86. doi: 10.1007/s10822-015-9888-6. Epub 2015 Dec 17.

44.

Incentives for Starting Small Companies Focused on Rare and Neglected Diseases.

Ekins S, Wood J.

Pharm Res. 2016 Apr;33(4):809-15. doi: 10.1007/s11095-015-1841-9. Epub 2015 Dec 14.

45.

Combining Metabolite-Based Pharmacophores with Bayesian Machine Learning Models for Mycobacterium tuberculosis Drug Discovery.

Ekins S, Madrid PB, Sarker M, Li SG, Mittal N, Kumar P, Wang X, Stratton TP, Zimmerman M, Talcott C, Bourbon P, Travers M, Yadav M, Freundlich JS.

PLoS One. 2015 Oct 30;10(10):e0141076. doi: 10.1371/journal.pone.0141076. eCollection 2015.

46.

Machine learning models identify molecules active against the Ebola virus in vitro.

Ekins S, Freundlich JS, Clark AM, Anantpadma M, Davey RA, Madrid P.

Version 3. F1000Res. 2015 Oct 20 [revised 2017 Jan 1];4:1091. doi: 10.12688/f1000research.7217.3. eCollection 2015.

47.

Kelch Domain of Gigaxonin Interacts with Intermediate Filament Proteins Affected in Giant Axonal Neuropathy.

Johnson-Kerner BL, Garcia Diaz A, Ekins S, Wichterle H.

PLoS One. 2015 Oct 13;10(10):e0140157. doi: 10.1371/journal.pone.0140157. eCollection 2015.

48.

Predicting Mouse Liver Microsomal Stability with "Pruned" Machine Learning Models and Public Data.

Perryman AL, Stratton TP, Ekins S, Freundlich JS.

Pharm Res. 2016 Feb;33(2):433-49. doi: 10.1007/s11095-015-1800-5. Epub 2015 Sep 28.

49.

Thermodynamic Proxies to Compensate for Biases in Drug Discovery Methods.

Ekins S, Litterman NK, Lipinski CA, Bunin BA.

Pharm Res. 2016 Jan;33(1):194-205. doi: 10.1007/s11095-015-1779-y. Epub 2015 Aug 27.

PMID:
26311555
50.

Evolution of a thienopyrimidine antitubercular relying on medicinal chemistry and metabolomics insights.

Li SG, Vilchèze C, Chakraborty S, Wang X, Kim H, Anisetti M, Ekins S, Rhee KY, Jacobs WR Jr, Freundlich JS.

Tetrahedron Lett. 2015 Jun 3;56(23):3246-3250.

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