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Items: 15

1.

Ensemble Docking in Drug Discovery: How Many Protein Configurations from Molecular Dynamics Simulations are Needed To Reproduce Known Ligand Binding?

Evangelista Falcon W, Ellingson SR, Smith JC, Baudry J.

J Phys Chem B. 2019 Feb 12. doi: 10.1021/acs.jpcb.8b11491. [Epub ahead of print]

PMID:
30695645
2.

Characterization of Squamous Cell Lung Cancers from Appalachian Kentucky.

Liu J, Murali T, Yu T, Liu C, Sivakumaran TA, Moseley HNB, Zhulin IB, Weiss HL, Durbin EB, Ellingson SR, Liu J, Huang B, Hallahan BJ, Horbinski CM, Hodges K, Napier DL, Bocklage T, Mueller J, Vanderford NL, Fardo DW, Wang C, Arnold SM.

Cancer Epidemiol Biomarkers Prev. 2019 Feb;28(2):348-356. doi: 10.1158/1055-9965.EPI-17-0984. Epub 2018 Oct 30.

PMID:
30377206
3.

Polypharmacology Within the Full Kinome: a Machine Learning Approach.

Jones D, Bopaiah J, Alghamedy F, Jacobs N, Weiss HL, de Jong WA, Ellingson SR.

AMIA Jt Summits Transl Sci Proc. 2018 May 18;2017:98-107. eCollection 2018.

4.

Incorporating Protein Dynamics Through Ensemble Docking in Machine Learning Models to Predict Drug Binding.

Alghamedy F, Bopaiah J, Jones D, Zhang X, Weiss HL, Ellingson SR.

AMIA Jt Summits Transl Sci Proc. 2018 May 18;2017:26-34. eCollection 2018.

5.

Gene-based association study of genes linked to hippocampal sclerosis of aging neuropathology: GRN, TMEM106B, ABCC9, and KCNMB2.

Katsumata Y, Nelson PT, Ellingson SR, Fardo DW.

Neurobiol Aging. 2017 May;53:193.e17-193.e25. doi: 10.1016/j.neurobiolaging.2017.01.003. Epub 2017 Jan 9.

6.

Genetic Comparison of Symptomatic and Asymptomatic Persons With Alzheimer Disease Neuropathology.

Monsell SE, Mock C, Fardo DW, Bertelsen S, Cairns NJ, Roe CM, Ellingson SR, Morris JC, Goate AM, Kukull WA.

Alzheimer Dis Assoc Disord. 2017 Jul-Sep;31(3):232-238. doi: 10.1097/WAD.0000000000000179.

7.

Automated quality control for genome wide association studies.

Ellingson SR, Fardo DW.

F1000Res. 2016 Jul 29;5:1889. doi: 10.12688/f1000research.9271.1. eCollection 2016.

8.

Ensemble-based docking: From hit discovery to metabolism and toxicity predictions.

Evangelista W, Weir RL, Ellingson SR, Harris JB, Kapoor K, Smith JC, Baudry J.

Bioorg Med Chem. 2016 Oct 15;24(20):4928-4935. doi: 10.1016/j.bmc.2016.07.064. Epub 2016 Jul 29.

9.

Reassessment of risk genotypes (GRN, TMEM106B, and ABCC9 variants) associated with hippocampal sclerosis of aging pathology.

Nelson PT, Wang WX, Partch AB, Monsell SE, Valladares O, Ellingson SR, Wilfred BR, Naj AC, Wang LS, Kukull WA, Fardo DW.

J Neuropathol Exp Neurol. 2015 Jan;74(1):75-84. doi: 10.1097/NEN.0000000000000151.

10.

Multi-conformer ensemble docking to difficult protein targets.

Ellingson SR, Miao Y, Baudry J, Smith JC.

J Phys Chem B. 2015 Jan 22;119(3):1026-34. doi: 10.1021/jp506511p. Epub 2014 Sep 24.

PMID:
25198248
11.

Accelerating Virtual High-Throughput Ligand Docking: current technology and case study on a petascale supercomputer.

Ellingson SR, Dakshanamurthy S, Brown M, Smith JC, Baudry J.

Concurr Comput. 2014 Apr 25;26(6):1268-1277.

12.

Detection of Bacillus anthracis DNA in complex soil and air samples using next-generation sequencing.

Be NA, Thissen JB, Gardner SN, McLoughlin KS, Fofanov VY, Koshinsky H, Ellingson SR, Brettin TS, Jackson PJ, Jaing CJ.

PLoS One. 2013 Sep 9;8(9):e73455. doi: 10.1371/journal.pone.0073455. eCollection 2013.

13.

VinaMPI: facilitating multiple receptor high-throughput virtual docking on high-performance computers.

Ellingson SR, Smith JC, Baudry J.

J Comput Chem. 2013 Sep 30;34(25):2212-21.

PMID:
23813626
14.

Known and novel post-transcriptional regulatory sequences are conserved across plant families.

Vaughn JN, Ellingson SR, Mignone F, Arnim Av.

RNA. 2012 Mar;18(3):368-84. doi: 10.1261/rna.031179.111. Epub 2012 Jan 11.

15.

Ammonia permeability of the soybean nodulin 26 channel.

Hwang JH, Ellingson SR, Roberts DM.

FEBS Lett. 2010 Oct 22;584(20):4339-43. doi: 10.1016/j.febslet.2010.09.033. Epub 2010 Sep 26.

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