2013 May 30
Seckler JM, Leioatts N, Miao H, Grossfield A. "The interplay of structure and dynamics: Insights from a survey of HIV-1 Reverse Transcriptase Crystal Structures." Proteins. 2013 May 30; Epub 2013 May 30.
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2013 Apr
Grossfield A. "Special issue on lipid-protein interactions." Chemistry and physics of lipids. 2013 Apr 0; 169:1.
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2012 Jul 10
Leioatts N, Romo TD, Grossfield A. "Elastic Network Models are Robust to Variations in Formalism." Journal of chemical theory and computation. 2012 Jul 10; 8(7):2424-2434. Epub 2012 Jun 05.
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2012 Mar 7
Olausson BE, Grossfield A, Pitman MC, Brown MF, Feller SE, Vogel A. "Molecular dynamics simulations reveal specific interactions of post-translational palmitoyl modifications with rhodopsin in membranes." Journal of the American Chemical Society. 2012 Mar 7; 134(9):4324-31. Epub 2012 Feb 22.
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2012 Feb
Horn JN, Sengillo JD, Lin D, Romo TD, Grossfield A. "Characterization of a potent antimicrobial lipopeptide via coarse-grained molecular dynamics." Biochimica et biophysica acta. 2012 Feb 0; 1818(2):212-8. Epub 2011 Jul 28.
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2011 Aug
Romo TD, Bradney LA, Greathouse DV, Grossfield A. "Membrane binding of an acyl-lactoferricin B antimicrobial peptide from solid-state NMR experiments and molecular dynamics simulations." Biochimica et biophysica acta. 2011 Aug 0; 1808(8):2019-30. Epub 2011 Apr 06.
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2011 Jul
Grossfield A. "Recent progress in the study of G protein-coupled receptors with molecular dynamics computer simulations." Biochimica et biophysica acta. 2011 Jul 0; 1808(7):1868-78. Epub 2011 Apr 03.
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2011 Jan
Romo TD, Grossfield A. "Validating and improving elastic network models with molecular dynamics simulations." Proteins. 2011 Jan 0; 79(1):23-34. Epub 2010 Sep 24.
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2010 Jun 4
Hurst DP, Grossfield A, Lynch DL, Feller S, Romo TD, Gawrisch K, Pitman MC, Reggio PH. "A lipid pathway for ligand binding is necessary for a cannabinoid G protein-coupled receptor." The Journal of biological chemistry. 2010 Jun 4; 285(23):17954-64. Epub 2010 Mar 10.
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2010 Jan 6
Romo TD, Grossfield A, Pitman MC. "Concerted interconversion between ionic lock substates of the beta(2) adrenergic receptor revealed by microsecond timescale molecular dynamics." Biophysical journal. 2010 Jan 6; 98(1):76-84.
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2009 Jan 1
Grossfield A, Zuckerman DM. "Quantifying uncertainty and sampling quality in biomolecular simulations." Annual reports in computational chemistry. 2009 Jan 1; 5:23-48.
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2009
Khelashvili, G.; Grossfield, A.; Feller, S. E.; Pitman, M. C.; Weinstein, H.;. "Structural and dynamic effects of cholesterol at preferred sites of interaction with rhodopsin identified from microsecond length molecular dynamics simulations". Proteins. 2009; 76(32): 403-17.
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2009
Romo TD, Grossfield A. "LOOS: an extensible platform for the structural analysis of simulations." Conference proceedings : ... Annual International Conference of the
IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine
and Biology Society. Conference. 2009 2009:2332-5.
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2008
Grossfield, A.; Pitman, M. C.; Feller, S. E.; Soubias, O.; Gawrisch, K.;. "Internal hydration increases during activation of the G-protein-coupled receptor rhodopsin". J Mol Biol. 2008; 381(32): 478-86.
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2007
Grossfield, A.; Feller, S. E.; Pitman, M. C.;. "Convergence of molecular dynamics simulations of membrane proteins". Proteins. 2007; 67(31): 31-40.
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2007
O'Neil L, L.; Grossfield, A.; Wiest, O.;. "Base Flipping of the Thymine Dimer in Duplex DNA". J Phys Chem B. 2007; .
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2007
Lau, P. W.; Grossfield, A.; Feller, S. E.; Pitman, M. C.; Brown, M. F.;. "Dynamic structure of retinylidene ligand of rhodopsin probed by molecular simulations". J Mol Biol. 2007; 372(34): 906-17.
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2006
Martinez-Mayorga, K.; Pitman, M. C.; Grossfield, A.; Feller, S. E.; Brown, M. F.;. "Retinal counterion switch mechanism in vision evaluated by molecular simulations". J Am Chem Soc. 2006; 128(351): 16502-3.
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2006
Grossfield, A.; Feller, S. E.; Pitman, M. C.;. "A role for direct interactions in the modulation of rhodopsin by omega-3 polyunsaturated lipids". Proc Natl Acad Sci U S A. 2006; 103(313): 4888-93.
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2006
Grossfield, A.; Feller, S. E.; Pitman, M. C.;. "Contribution of omega-3 fatty acids to the thermodynamics of membrane protein solvation". J Phys Chem B. 2006; 110(318): 8907-9.
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2006
Jiao, D.; King, C.; Grossfield, A.; Darden, T. A.; Ren, P.;. "Simulation of Ca2+ and Mg2+ solvation using polarizable atomic multipole potential". J Phys Chem B. 2006; 110(337): 18553-9.
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2005
Pitman, M. C.; Grossfield, A.; Suits, F.; Feller, S. E.;. "Role of cholesterol and polyunsaturated chains in lipid-protein interactions: molecular dynamics simulation of rhodopsin in a realistic membrane environment". J Am Chem Soc. 2005; 127(313): 4576-7.
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2005
Grossfield, A.;. "Dependence of ion hydration on the sign of the ion's charge". J Chem Phys. 2005; 122(32): 024506.
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2004
Drozdov, A. N.; Grossfield, A.; Pappu, R. V.;. "Role of solvent in determining conformational preferences of alanine dipeptide in water". J Am Chem Soc. 2004; 126(38): 2574-81.
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2003
Grossfield, A.; Ren, P.; Ponder, J. W.;. "Ion solvation thermodynamics from simulation with a polarizable force field". J Am Chem Soc. 2003; 125(350): 15671-82.
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2000
Woolf, T. B.; Grossfield, A.; Tychko, M.;. "Differences between apo and three holo forms of the intestinal fatty acid binding protein seen by molecular dynamics computer calculations". Biophys J. 2000; 78(32): 608-25.
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2000
Grossfield, A.; Sachs, J.; Woolf, T. B.;. "Dipole lattice membrane model for protein calculations". Proteins. 2000; 41(32): 211-23.
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2000
Petrache, H. I.; Grossfield, A.; MacKenzie, K. R.; Engelman, D. M.; Woolf, T. B.;. "Modulation of glycophorin A transmembrane helix interactions by lipid bilayers: molecular dynamics calculations". J Mol Biol. 2000; 302(33): 727-46.
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