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GROMACS: fast, flexible, and free.
J Comput Chem. 2005 Dec;26(16):1701-18
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Allosteric functioning of dimeric class C G-protein-coupled receptors.
FEBS J. 2005 Jun;272(12):2947-55
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Lipid-mediated interactions tune the association of glycophorin A helix and its disruptive mutants in membranes.
Phys Chem Chem Phys. 2010 Oct 28;12(40):12987-96
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Formation and dissociation of M1 muscarinic receptor dimers seen by total internal reflection fluorescence imaging of single molecules.
Proc Natl Acad Sci U S A. 2010 Feb 9;107(6):2693-8
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A rigorous experimental framework for detecting protein oligomerization using bioluminescence resonance energy transfer.
Nat Methods. 2006 Dec;3(12):1001-6
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Monomeric G-protein-coupled receptor as a functional unit.
Biochemistry. 2005 Jul 12;44(27):9395-403
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Lipid packing drives the segregation of transmembrane helices into disordered lipid domains in model membranes.
Proc Natl Acad Sci U S A. 2011 Jan 25;108(4):1343-8
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Efficient coupling of transducin to monomeric rhodopsin in a phospholipid bilayer.
J Biol Chem. 2008 Feb 15;283(7):4387-94
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Structural determinants of the supramolecular organization of G protein-coupled receptors in bilayers.
J Am Chem Soc. 2012 Jul 4;134(26):10959-65
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Well-tempered metadynamics: a smoothly converging and tunable free-energy method.
Phys Rev Lett. 2008 Jan 18;100(2):020603
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Transducin activation by nanoscale lipid bilayers containing one and two rhodopsins.
J Biol Chem. 2007 May 18;282(20):14875-81
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Setting up and running molecular dynamics simulations of membrane proteins.
Methods. 2007 Apr;41(4):475-88
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Increasingly accurate dynamic molecular models of G-protein coupled receptor oligomers: Panacea or Pandora's box for novel drug discovery?
Life Sci. 2010 Apr 10;86(15-16):590-7
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Protein-protein docking with backbone flexibility.
J Mol Biol. 2007 Oct 19;373(2):503-19
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The MARTINI Coarse-Grained Force Field: Extension to Proteins.
J Chem Theory Comput. 2008 May;4(5):819-34
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Ligand-regulated oligomerization of beta(2)-adrenoceptors in a model lipid bilayer.
EMBO J. 2009 Nov 4;28(21):3315-28
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Fast procedure for reconstruction of full-atom protein models from reduced representations.
J Comput Chem. 2008 Jul 15;29(9):1460-5
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Full characterization of GPCR monomer-dimer dynamic equilibrium by single molecule imaging.
J Cell Biol. 2011 Feb 7;192(3):463-80
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Experimental challenge to a 'rigorous' BRET analysis of GPCR oligomerization.
Nat Methods. 2007 Aug;4(8):599-600; author reply 601
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Lessons from free energy simulations of delta-opioid receptor homodimers involving the fourth transmembrane helix.
Biochemistry. 2010 Aug 10;49(31):6771-6
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Molecular determinants and thermodynamics of the amyloid precursor protein transmembrane domain implicated in Alzheimer's disease.
J Mol Biol. 2011 May 20;408(5):879-95
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Rhodopsin forms a dimer with cytoplasmic helix 8 contacts in native membranes.
Biochemistry. 2012 Mar 6;51(9):1819-21
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Dimerization of Amino Acid Side Chains: Lessons from the Comparison of Different Force Fields.
J Chem Theory Comput. 2012 Mar 13;8(3):1003-14
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GPCR monomers and oligomers: it takes all kinds.
Trends Neurosci. 2008 Feb;31(2):74-81
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Structures of the CXCR4 chemokine GPCR with small-molecule and cyclic peptide antagonists.
Science. 2010 Nov 19;330(6007):1066-71
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Conformational changes in the G protein Gs induced by the β2 adrenergic receptor.
Nature. 2011 Sep 28;477(7366):611-5
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Crystal structure of the µ-opioid receptor bound to a morphinan antagonist.
Nature. 2012 Mar 21;485(7398):321-6
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FRET imaging reveals that functional neurokinin-1 receptors are monomeric and reside in membrane microdomains of live cells.
Proc Natl Acad Sci U S A. 2006 Feb 14;103(7):2138-43
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High-resolution crystal structure of an engineered human beta2-adrenergic G protein-coupled receptor.
Science. 2007 Nov 23;318(5854):1258-65
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Dopamine D2 receptors form higher order oligomers at physiological expression levels.
EMBO J. 2008 Sep 3;27(17):2293-304
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Modeller: generation and refinement of homology-based protein structure models.
Methods Enzymol. 2003;374:461-91
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Reconstructing the equilibrium Boltzmann distribution from well-tempered metadynamics.
J Comput Chem. 2009 Aug;30(11):1615-21
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G protein-coupled receptors self-assemble in dynamics simulations of model bilayers.
J Am Chem Soc. 2007 Aug 22;129(33):10126-32
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Convergence and error estimation in free energy calculations using the weighted histogram analysis method.
J Comput Chem. 2012 Feb 5;33(4):453-65
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Combining an Elastic Network With a Coarse-Grained Molecular Force Field: Structure, Dynamics, and Intermolecular Recognition.
J Chem Theory Comput. 2009 Sep 8;5(9):2531-43
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A day in the life of a G protein-coupled receptor: the contribution to function of G protein-coupled receptor dimerization.
Br J Pharmacol. 2008 Mar;153 Suppl 1:S216-29
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Making structural sense of dimerization interfaces of delta opioid receptor homodimers.
Biochemistry. 2011 Mar 15;50(10):1682-90
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Effect of urea on the β-hairpin conformational ensemble and protein denaturation mechanism.
J Am Chem Soc. 2011 Nov 2;133(43):17200-6
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Analysis of receptor oligomerization by FRAP microscopy.
Nat Methods. 2009 Mar;6(3):225-30
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Structure of a beta1-adrenergic G-protein-coupled receptor.
Nature. 2008 Jul 24;454(7203):486-91
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Instability of a class a G protein-coupled receptor oligomer interface.
Mol Pharmacol. 2009 Jun;75(6):1296-9
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Energetics of ion conduction through the gramicidin channel.
Proc Natl Acad Sci U S A. 2004 Jan 6;101(1):117-22
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The MARTINI force field: coarse grained model for biomolecular simulations.
J Phys Chem B. 2007 Jul 12;111(27):7812-24
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