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Items: 1 to 20 of 133

1.

Water network perturbation in ligand binding: adenosine A(2A) antagonists as a case study.

Bortolato A, Tehan BG, Bodnarchuk MS, Essex JW, Mason JS.

J Chem Inf Model. 2013 Jul 22;53(7):1700-13. doi: 10.1021/ci4001458. Epub 2013 Jun 14.

PMID:
23725291
2.

Perturbation of fluid dynamics properties of water molecules during G protein-coupled receptor-ligand recognition: the human A2A adenosine receptor as a key study.

Sabbadin D, Ciancetta A, Moro S.

J Chem Inf Model. 2014 Oct 27;54(10):2846-55. doi: 10.1021/ci500397y. Epub 2014 Oct 6.

PMID:
25245783
3.

Bridging molecular docking to membrane molecular dynamics to investigate GPCR-ligand recognition: the human A₂A adenosine receptor as a key study.

Sabbadin D, Ciancetta A, Moro S.

J Chem Inf Model. 2014 Jan 27;54(1):169-83. doi: 10.1021/ci400532b. Epub 2014 Jan 8.

PMID:
24359090
4.

Complementarity between in silico and biophysical screening approaches in fragment-based lead discovery against the A(2A) adenosine receptor.

Chen D, Ranganathan A, IJzerman AP, Siegal G, Carlsson J.

J Chem Inf Model. 2013 Oct 28;53(10):2701-14. doi: 10.1021/ci4003156. Epub 2013 Sep 18.

PMID:
23971943
5.

Selecting an optimal number of binding site waters to improve virtual screening enrichments against the adenosine A2A receptor.

Lenselink EB, Beuming T, Sherman W, van Vlijmen HW, IJzerman AP.

J Chem Inf Model. 2014 Jun 23;54(6):1737-46. doi: 10.1021/ci5000455. Epub 2014 Jun 3.

PMID:
24835542
6.

Novel adenosine A(2A) receptor ligands: a synthetic, functional and computational investigation of selected literature adenosine A(2A) receptor antagonists for extending into extracellular space.

Jörg M, Shonberg J, Mak FS, Miller ND, Yuriev E, Scammells PJ, Capuano B.

Bioorg Med Chem Lett. 2013 Jun 1;23(11):3427-33. doi: 10.1016/j.bmcl.2013.03.070. Epub 2013 Apr 2.

PMID:
23602401
7.

Structural and energetic effects of A2A adenosine receptor mutations on agonist and antagonist binding.

Keränen H, Gutiérrez-de-Terán H, Åqvist J.

PLoS One. 2014 Oct 6;9(10):e108492. doi: 10.1371/journal.pone.0108492. eCollection 2014.

8.

Revisiting a receptor-based pharmacophore hypothesis for human A(2A) adenosine receptor antagonists.

Bacilieri M, Ciancetta A, Paoletta S, Federico S, Cosconati S, Cacciari B, Taliani S, Da Settimo F, Novellino E, Klotz KN, Spalluto G, Moro S.

J Chem Inf Model. 2013 Jul 22;53(7):1620-37. doi: 10.1021/ci300615u. Epub 2013 Jun 20.

PMID:
23705857
9.

Substructure-based virtual screening for adenosine A2A receptor ligands.

van der Horst E, van der Pijl R, Mulder-Krieger T, Bender A, Ijzerman AP.

ChemMedChem. 2011 Dec 9;6(12):2302-11. doi: 10.1002/cmdc.201100369. Epub 2011 Oct 21.

PMID:
22021213
10.

Carbohydrate-binding proteins: Dissecting ligand structures through solvent environment occupancy.

Gauto DF, Di Lella S, Guardia CM, Estrin DA, Martí MA.

J Phys Chem B. 2009 Jun 25;113(25):8717-24. doi: 10.1021/jp901196n.

PMID:
19485380
11.

Biophysical mapping of the adenosine A2A receptor.

Zhukov A, Andrews SP, Errey JC, Robertson N, Tehan B, Mason JS, Marshall FH, Weir M, Congreve M.

J Med Chem. 2011 Jul 14;54(13):4312-23. doi: 10.1021/jm2003798. Epub 2011 Jun 10.

12.

Synthesis and SAR studies of analogues of 4-(3,3-dimethyl-butyrylamino)-3,5-difluoro-N-thiazol-2-yl-benzamide (Lu AA41063) as adenosine A2A receptor ligands with improved aqueous solubility.

Mikkelsen GK, Langgård M, Schrøder TJ, Kreilgaard M, Jørgensen EB, Brandt G, Griffon Y, Boffey R, Bang-Andersen B.

Bioorg Med Chem Lett. 2015 Mar 15;25(6):1212-6. doi: 10.1016/j.bmcl.2015.01.062. Epub 2015 Feb 7.

PMID:
25701253
13.

Classification of water molecules in protein binding sites.

Barillari C, Taylor J, Viner R, Essex JW.

J Am Chem Soc. 2007 Mar 7;129(9):2577-87. Epub 2007 Feb 9.

PMID:
17288418
14.

Computation of binding free energy with molecular dynamics and grand canonical Monte Carlo simulations.

Deng Y, Roux B.

J Chem Phys. 2008 Mar 21;128(11):115103. doi: 10.1063/1.2842080.

PMID:
18361618
15.

Real-time monitoring of binding events on a thermostabilized human A2A receptor embedded in a lipid bilayer by surface plasmon resonance.

Bocquet N, Kohler J, Hug MN, Kusznir EA, Rufer AC, Dawson RJ, Hennig M, Ruf A, Huber W, Huber S.

Biochim Biophys Acta. 2015 May;1848(5):1224-33. doi: 10.1016/j.bbamem.2015.02.014. Epub 2015 Feb 25.

16.

A water-swap reaction coordinate for the calculation of absolute protein-ligand binding free energies.

Woods CJ, Malaisree M, Hannongbua S, Mulholland AJ.

J Chem Phys. 2011 Feb 7;134(5):054114. doi: 10.1063/1.3519057.

PMID:
21303099
17.

Isothermal chemical denaturation to determine binding affinity of small molecules to G-protein coupled receptors.

Ross P, Weihofen W, Siu F, Xie A, Katakia H, Wright SK, Hunt I, Brown RK, Freire E.

Anal Biochem. 2015 Mar 15;473:41-5. doi: 10.1016/j.ab.2014.11.019. Epub 2014 Dec 4.

18.

Towards predictive ligand design with free-energy based computational methods?

Foloppe N, Hubbard R.

Curr Med Chem. 2006;13(29):3583-608.

PMID:
17168725
19.

Prediction of ligand binding affinity and orientation of xenoestrogens to the estrogen receptor by molecular dynamics simulations and the linear interaction energy method.

van Lipzig MM, ter Laak AM, Jongejan A, Vermeulen NP, Wamelink M, Geerke D, Meerman JH.

J Med Chem. 2004 Feb 12;47(4):1018-30.

PMID:
14761204
20.

Grand canonical Monte Carlo simulation of ligand-protein binding.

Clark M, Guarnieri F, Shkurko I, Wiseman J.

J Chem Inf Model. 2006 Jan-Feb;46(1):231-42.

PMID:
16426059

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