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Items: 1 to 50 of 60

1.

Molecular determinants of the differential modulation of Cav1.2 and Cav1.3 by nifedipine and FPL 64176.

Wang Y, Tang S, Harvey KE, Salyer AE, Li TA, Rantz EK, Lill MA, Hockerman GH.

Mol Pharmacol. 2018 Jul 6. pii: mol.118.112441. doi: 10.1124/mol.118.112441. [Epub ahead of print]

2.

Calculation of Thermodynamic Properties of Bound Water Molecules.

Yang Y, Abdallah AHA, Lill MA.

Methods Mol Biol. 2018;1762:389-402. doi: 10.1007/978-1-4939-7756-7_19.

PMID:
29594782
3.

WATsite2.0 with PyMOL Plugin: Hydration Site Prediction and Visualization.

Yang Y, Hu B, Lill MA.

Methods Mol Biol. 2017;1611:123-134. doi: 10.1007/978-1-4939-7015-5_10.

PMID:
28451976
4.

Molecular Modeling Evaluation of the Enantiomers of a Novel Adenylyl Cyclase 2 Inhibitor.

Rana N, Conley JM, Soto-Velasquez M, León F, Cutler SJ, Watts VJ, Lill MA.

J Chem Inf Model. 2017 Feb 27;57(2):322-334. doi: 10.1021/acs.jcim.6b00454. Epub 2017 Jan 26.

PMID:
28068084
5.

Confined Mobility of TonB and FepA in Escherichia coli Membranes.

Lill Y, Jordan LD, Smallwood CR, Newton SM, Lill MA, Klebba PE, Ritchie K.

PLoS One. 2016 Dec 9;11(12):e0160862. doi: 10.1371/journal.pone.0160862. eCollection 2016.

6.

Fibpredictor: a computational method for rapid prediction of amyloid fibril structures.

Tabatabaei Ghomi H, Topp EM, Lill MA.

J Mol Model. 2016 Sep;22(9):206. doi: 10.1007/s00894-016-3066-1. Epub 2016 Aug 8.

PMID:
27502172
7.

Dissecting the Influence of Protein Flexibility on the Location and Thermodynamic Profile of Explicit Water Molecules in Protein-Ligand Binding.

Yang Y, Lill MA.

J Chem Theory Comput. 2016 Sep 13;12(9):4578-92. doi: 10.1021/acs.jctc.6b00411. Epub 2016 Aug 18.

8.

Ranking protein-protein docking results using steered molecular dynamics and potential of mean force calculations.

Kingsley LJ, Esquivel-Rodríguez J, Yang Y, Kihara D, Lill MA.

J Comput Chem. 2016 Jul;37(20):1861-5. doi: 10.1002/jcc.24412. Epub 2016 May 27.

9.

Structural transitions and interactions in the early stages of human glucagon amyloid fibrillation.

Moorthy BS, Ghomi HT, Lill MA, Topp EM.

Biophys J. 2015 Feb 17;108(4):937-948. doi: 10.1016/j.bpj.2015.01.004.

10.

Substrate tunnels in enzymes: structure-function relationships and computational methodology.

Kingsley LJ, Lill MA.

Proteins. 2015 Apr;83(4):599-611. doi: 10.1002/prot.24772. Epub 2015 Feb 28. Review.

11.
12.

Analysis of factors influencing hydration site prediction based on molecular dynamics simulations.

Yang Y, Hu B, Lill MA.

J Chem Inf Model. 2014 Oct 27;54(10):2987-95. doi: 10.1021/ci500426q. Epub 2014 Oct 7.

13.

Are distance-dependent statistical potentials considering three interacting bodies superior to two-body statistical potentials for protein structure prediction?

Ghomi HT, Thompson JJ, Lill MA.

J Bioinform Comput Biol. 2014 Oct;12(5):1450022. doi: 10.1142/S021972001450022X. Epub 2014 Sep 11.

PMID:
25212727
14.

Combining structure- and ligand-based approaches to improve site of metabolism prediction in CYP2C9 substrates.

Kingsley LJ, Wilson GL, Essex ME, Lill MA.

Pharm Res. 2015 Mar;32(3):986-1001. doi: 10.1007/s11095-014-1511-3. Epub 2014 Sep 11.

15.

Including ligand-induced protein flexibility into protein tunnel prediction.

Kingsley LJ, Lill MA.

J Comput Chem. 2014 Sep 15;35(24):1748-56. doi: 10.1002/jcc.23680. Epub 2014 Jul 5.

16.

Flexibility of PCNA-protein interface accommodates differential binding partners.

Pedley AM, Lill MA, Davisson VJ.

PLoS One. 2014 Jul 18;9(7):e102481. doi: 10.1371/journal.pone.0102481. eCollection 2014.

17.

Ensemble generation and the influence of protein flexibility on geometric tunnel prediction in cytochrome P450 enzymes.

Kingsley LJ, Lill MA.

PLoS One. 2014 Jun 23;9(6):e99408. doi: 10.1371/journal.pone.0099408. eCollection 2014.

18.

WATsite: hydration site prediction program with PyMOL interface.

Hu B, Lill MA.

J Comput Chem. 2014 Jun 15;35(16):1255-60. doi: 10.1002/jcc.23616. Epub 2014 Apr 22.

19.

PharmDock: a pharmacophore-based docking program.

Hu B, Lill MA.

J Cheminform. 2014 Apr 16;6:14. doi: 10.1186/1758-2946-6-14. eCollection 2014.

20.

Metrics for measuring distances in configuration spaces.

Sadeghi A, Ghasemi SA, Schaefer B, Mohr S, Lill MA, Goedecker S.

J Chem Phys. 2013 Nov 14;139(18):184118. doi: 10.1063/1.4828704.

PMID:
24320265
21.

Induced fit docking, and the use of QM/MM methods in docking.

Xu M, Lill MA.

Drug Discov Today Technol. 2013 Sep;10(3):e411-8. doi: 10.1016/j.ddtec.2013.02.003. Review.

22.

Exploring the potential of protein-based pharmacophore models in ligand pose prediction and ranking.

Hu B, Lill MA.

J Chem Inf Model. 2013 May 24;53(5):1179-90. doi: 10.1021/ci400143r. Epub 2013 May 13.

23.

Stabilization of an unusual salt bridge in ubiquitin by the extra C-terminal domain of the proteasome-associated deubiquitinase UCH37 as a mechanism of its exo specificity.

Morrow ME, Kim MI, Ronau JA, Sheedlo MJ, White RR, Chaney J, Paul LN, Lill MA, Artavanis-Tsakonas K, Das C.

Biochemistry. 2013 May 21;52(20):3564-78. doi: 10.1021/bi4003106. Epub 2013 May 9.

24.

Extensive rigid analogue design maps the binding conformation of potent N-benzylphenethylamine 5-HT2A serotonin receptor agonist ligands.

Juncosa JI Jr, Hansen M, Bonner LA, Cueva JP, Maglathlin R, McCorvy JD, Marona-Lewicka D, Lill MA, Nichols DE.

ACS Chem Neurosci. 2013 Jan 16;4(1):96-109. doi: 10.1021/cn3000668. Epub 2012 Jul 17.

25.

Towards a Realistic Representation in Surface-Based Pseudoreceptor Modeling: a PDB-Wide Analysis of Binding Pockets.

Wilson GL, Lill MA.

Mol Inform. 2012 Apr;31(3-4):259-71. doi: 10.1002/minf.201100166. Epub 2012 Mar 14.

PMID:
27477096
26.

Protein pharmacophore selection using hydration-site analysis.

Hu B, Lill MA.

J Chem Inf Model. 2012 Apr 23;52(4):1046-60. doi: 10.1021/ci200620h. Epub 2012 Mar 26.

27.

Analogues of doxanthrine reveal differences between the dopamine D1 receptor binding properties of chromanoisoquinolines and hexahydrobenzo[a]phenanthridines.

Cueva JP, Chemel BR, Juncosa JI Jr, Lill MA, Watts VJ, Nichols DE.

Eur J Med Chem. 2012 Feb;48:97-107. doi: 10.1016/j.ejmech.2011.11.039. Epub 2011 Dec 3.

28.

Utilizing experimental data for reducing ensemble size in flexible-protein docking.

Xu M, Lill MA.

J Chem Inf Model. 2012 Jan 23;52(1):187-98. doi: 10.1021/ci200428t. Epub 2011 Dec 19.

29.

Predicting flexible loop regions that interact with ligands: the challenge of accurate scoring.

Danielson ML, Lill MA.

Proteins. 2012 Jan;80(1):246-60. doi: 10.1002/prot.23199. Epub 2011 Nov 9.

30.

Solvent interaction energy calculations on molecular dynamics trajectories: increasing the efficiency using systematic frame selection.

Lill MA, Thompson JJ.

J Chem Inf Model. 2011 Oct 24;51(10):2680-9. doi: 10.1021/ci200191m. Epub 2011 Sep 15.

31.

Probing the steric space at the floor of the D1 dopamine receptor orthosteric binding domain: 7α-, 7β-, 8α-, and 8β-methyl substituted dihydrexidine analogues.

Cueva JP, Gallardo-Godoy A, Juncosa JI, Vidi PA, Lill MA, Watts VJ, Nichols DE.

J Med Chem. 2011 Aug 11;54(15):5508-21. doi: 10.1021/jm200334c. Epub 2011 Jul 14.

32.

Potentially increasing the metabolic stability of drug candidates via computational site of metabolism prediction by CYP2C9: The utility of incorporating protein flexibility via an ensemble of structures.

Danielson ML, Desai PV, Mohutsky MA, Wrighton SA, Lill MA.

Eur J Med Chem. 2011 Sep;46(9):3953-63. doi: 10.1016/j.ejmech.2011.05.067. Epub 2011 Jun 23.

33.

Efficient incorporation of protein flexibility and dynamics into molecular docking simulations.

Lill MA.

Biochemistry. 2011 Jul 19;50(28):6157-69. doi: 10.1021/bi2004558. Epub 2011 Jun 22. Review.

34.

Integrating structure-based and ligand-based approaches for computational drug design.

Wilson GL, Lill MA.

Future Med Chem. 2011 Apr;3(6):735-50. doi: 10.4155/fmc.11.18. Review.

PMID:
21554079
35.

Mapping the catechol binding site in dopamine D₁ receptors: synthesis and evaluation of two parallel series of bicyclic dopamine analogues.

Bonner LA, Laban U, Chemel BR, Juncosa JI, Lill MA, Watts VJ, Nichols DE.

ChemMedChem. 2011 Jun 6;6(6):1024-40. doi: 10.1002/cmdc.201100010. Epub 2011 Apr 28.

36.

Significant enhancement of docking sensitivity using implicit ligand sampling.

Xu M, Lill MA.

J Chem Inf Model. 2011 Mar 28;51(3):693-706. doi: 10.1021/ci100457t. Epub 2011 Mar 4.

37.

Computer-aided drug design platform using PyMOL.

Lill MA, Danielson ML.

J Comput Aided Mol Des. 2011 Jan;25(1):13-9. doi: 10.1007/s10822-010-9395-8. Epub 2010 Oct 30.

PMID:
21053052
38.

New computational method for prediction of interacting protein loop regions.

Danielson ML, Lill MA.

Proteins. 2010 May 15;78(7):1748-59. doi: 10.1002/prot.22690.

PMID:
20186974
39.

Challenges predicting ligand-receptor interactions of promiscuous proteins: the nuclear receptor PXR.

Ekins S, Kortagere S, Iyer M, Reschly EJ, Lill MA, Redinbo MR, Krasowski MD.

PLoS Comput Biol. 2009 Dec;5(12):e1000594. doi: 10.1371/journal.pcbi.1000594. Epub 2009 Dec 11.

40.

Long-chain carboxychromanols, metabolites of vitamin E, are potent inhibitors of cyclooxygenases.

Jiang Q, Yin X, Lill MA, Danielson ML, Freiser H, Huang J.

Proc Natl Acad Sci U S A. 2008 Dec 23;105(51):20464-9. doi: 10.1073/pnas.0810962106. Epub 2008 Dec 11.

41.

Mixed-model QSAR at the glucocorticoid receptor: predicting the binding mode and affinity of psychotropic drugs.

Spreafico M, Ernst B, Lill MA, Smiesko M, Vedani A.

ChemMedChem. 2009 Jan;4(1):100-9. doi: 10.1002/cmdc.200800274.

PMID:
19009570
42.

Multi-dimensional QSAR in drug discovery.

Lill MA.

Drug Discov Today. 2007 Dec;12(23-24):1013-7. Epub 2007 Sep 19. Review.

PMID:
18061879
43.

A bifunctional colchicinoid that binds to the androgen receptor.

Sharifi N, Hamel E, Lill MA, Risbood P, Kane CT Jr, Hossain MT, Jones A, Dalton JT, Farrar WL.

Mol Cancer Ther. 2007 Aug;6(8):2328-36.

44.

Predicting the toxic potential of drugs and chemicals in silico.

Vedani A, Lill MA, Dobler M.

ALTEX. 2007;24 Spec No:63-6.

PMID:
19835061
45.
46.
47.

The challenge of predicting drug toxicity in silico.

Vedani A, Dobler M, Lill MA.

Basic Clin Pharmacol Toxicol. 2006 Sep;99(3):195-208. Review.

48.
49.

Single hepatitis-B virus core capsid binding to individual nuclear pore complexes in Hela cells.

Lill Y, Lill MA, Fahrenkrog B, Schwarz-Herion K, Paulillo S, Aebi U, Hecht B.

Biophys J. 2006 Oct 15;91(8):3123-30. Epub 2006 Jul 28.

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