Alan M. Grossfield, Ph.D.

Alan M. Grossfield, Ph.D.

Contact Information

University of Rochester Medical Center
School of Medicine and Dentistry
601 Elmwood Ave, Box 712
Rochester, NY 14642

Office: (585) 276-4193
Fax: (585) 275-6007

Journal Articles

Showing all 43 journal articles available.

2015 Aug 18
Lin D, Grossfield A. "Thermodynamics of Micelle Formation and Membrane Fusion Modulate Antimicrobial Lipopeptide Activity." Biophysical journal. 2015 Aug 18; 109(4):750-9.
2015 Aug 4
Leioatts N, Romo TD, Danial SA, Grossfield A. "Retinal Conformation Changes Rhodopsin's Dynamic Ensemble." Biophysical journal. 2015 Aug 4; 109(3):608-17.
Aytenfisu AH, Spasic A, Grossfield A, Stern H, Mathews DH. "99 Improving the amber RNA force field." Journal of biomolecular structure & dynamics. 2015 33 Suppl 1:63.
2014 Dec 15
Romo TD, Leioatts N, Grossfield A. "Lightweight object oriented structure analysis: tools for building tools to analyze molecular dynamics simulations." Journal of computational chemistry. 2014 Dec 15; 35(32):2305-18. Epub 2014 Oct 18.
2014 Oct 21
Lin D, Grossfield A. "Thermodynamics of antimicrobial lipopeptide binding to membranes: origins of affinity and selectivity." Biophysical journal. 2014 Oct 21; 107(8):1862-72.
2014 Oct
Leioatts N, Suresh P, Romo TD, Grossfield A. "Structure-based simulations reveal concerted dynamics of GPCR activation." Proteins. 2014 Oct; 82(10):2538-51. Epub 2014 Jun 09.
2014 Jul 18
Mnpotra JS, Qiao Z, Cai J, Lynch DL, Grossfield A, Leioatts N, Hurst DP, Pitman MC, Song ZH, Reggio PH. "Structural basis of G protein-coupled receptor-Gi protein interaction: formation of the cannabinoid CB2 receptor-Gi protein complex." The Journal of biological chemistry. 2014 Jul 18; 289(29):20259-72. Epub 2014 May 22.
2014 Jun 17
Romo TD, Grossfield A. "How fast is your camera? Timescales for molecular motion and their role in restraining molecular dynamics." Biophysical journal. 2014 Jun 17; 106(12):2549-51.
2014 Apr 15
Romo TD, Grossfield A. "Unknown unknowns: the challenge of systematic and statistical error in molecular dynamics simulations." Biophysical journal. 2014 Apr 15; 106(8):1553-4.
2014 Mar
Kimura T, Vukoti K, Lynch DL, Hurst DP, Grossfield A, Pitman MC, Reggio PH, Yeliseev AA, Gawrisch K. "Global fold of human cannabinoid type 2 receptor probed by solid-state 13C-, 15N-MAS NMR and molecular dynamics simulations." Proteins. 2014 Mar; 82(3):452-65. Epub 2013 Oct 17.
2014 Jan 21
Leioatts N, Mertz B, Martinez-Mayorga K, Romo TD, Pitman MC, Feller SE, Grossfield A, Brown MF. "Retinal ligand mobility explains internal hydration and reconciles active rhodopsin structures." Biochemistry. 2014 Jan 21; 53(2):376-85. Epub 2014 Jan 08.
Horn JN, Kao TC, Grossfield A. "Coarse-grained molecular dynamics provides insight into the interactions of lipids and cholesterol with rhodopsin." Advances in experimental medicine and biology. 2014 796:75-94.
2013 Oct 1
Horn JN, Cravens A, Grossfield A. "Interactions between fengycin and model bilayers quantified by coarse-grained molecular dynamics." Biophysical journal. 2013 Oct 1; 105(7):1612-23.
2013 Oct
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 Oct; 81(10):1792-801. Epub 2013 Aug 16.
2013 Aug 20
Horn JN, Romo TD, Grossfield A. "Simulating the mechanism of antimicrobial lipopeptides with all-atom molecular dynamics." Biochemistry. 2013 Aug 20; 52(33):5604-10. Epub 2013 Aug 09.
2013 Apr
Grossfield A. "Special issue on lipid-protein interactions." Chemistry and physics of lipids. 2013 Apr; 169:1.
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.
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.
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; 1818(2):212-8. Epub 2011 Jul 28.
2011 Aug 9
Romo TD, Grossfield A. "Block Covariance Overlap Method and Convergence in Molecular Dynamics Simulation." Journal of chemical theory and computation. 2011 Aug 9; 7(8):2464-72. Epub 2011 Jul 01.
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; 1808(8):2019-30. Epub 2011 Apr 06.
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; 1808(7):1868-78. Epub 2011 Apr 03.
2011 Jan
Romo TD, Grossfield A. "Validating and improving elastic network models with molecular dynamics simulations." Proteins. 2011 Jan; 79(1):23-34. Epub 2010 Sep 24.
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.
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.
2009 Aug 1
Khelashvili G, Grossfield A, Feller SE, Pitman MC, Weinstein H. "Structural and dynamic effects of cholesterol at preferred sites of interaction with rhodopsin identified from microsecond length molecular dynamics simulations." Proteins. 2009 Aug 1; 76(2):403-17.
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.
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. 2009 2009:2332-5.
2008 Aug 29
Grossfield A, Pitman MC, Feller SE, Soubias O, Gawrisch K. "Internal hydration increases during activation of the G-protein-coupled receptor rhodopsin." Journal of molecular biology. 2008 Aug 29; 381(2):478-86. Epub 2008 May 22.
2007 Oct 11
O'Neil LL, Grossfield A, Wiest O. "Base flipping of the thymine dimer in duplex DNA." The journal of physical chemistry. B. 2007 Oct 11; 111(40):11843-9. Epub 2007 Sep 15.
2007 Sep 28
Lau PW, Grossfield A, Feller SE, Pitman MC, Brown MF. "Dynamic structure of retinylidene ligand of rhodopsin probed by molecular simulations." Journal of molecular biology. 2007 Sep 28; 372(4):906-17. Epub 2007 Jun 26.
2007 Apr 1
Grossfield A, Feller SE, Pitman MC. "Convergence of molecular dynamics simulations of membrane proteins." Proteins. 2007 Apr 1; 67(1):31-40.
2006 Dec 27
Martínez-Mayorga K, Pitman MC, Grossfield A, Feller SE, Brown MF. "Retinal counterion switch mechanism in vision evaluated by molecular simulations." Journal of the American Chemical Society. 2006 Dec 27; 128(51):16502-3.
2006 Sep 21
Jiao D, King C, Grossfield A, Darden TA, Ren P. "Simulation of Ca2+ and Mg2+ solvation using polarizable atomic multipole potential." The journal of physical chemistry. B. 2006 Sep 21; 110(37):18553-9.
2006 May 11
Grossfield A, Feller SE, Pitman MC. "Contribution of omega-3 fatty acids to the thermodynamics of membrane protein solvation." The journal of physical chemistry. B. 2006 May 11; 110(18):8907-9.
2006 Mar 28
Grossfield A, Feller SE, Pitman MC. "A role for direct interactions in the modulation of rhodopsin by omega-3 polyunsaturated lipids." Proceedings of the National Academy of Sciences of the United States of America. 2006 Mar 28; 103(13):4888-93. Epub 2006 Mar 17.
2005 Apr 6
Pitman MC, Grossfield A, Suits F, Feller SE. "Role of cholesterol and polyunsaturated chains in lipid-protein interactions: molecular dynamics simulation of rhodopsin in a realistic membrane environment." Journal of the American Chemical Society. 2005 Apr 6; 127(13):4576-7.
2005 Jan 8
Grossfield A. "Dependence of ion hydration on the sign of the ion's charge." The Journal of chemical physics. 2005 Jan 8; 122(2):024506.
2004 Mar 3
Drozdov AN, Grossfield A, Pappu RV. "Role of solvent in determining conformational preferences of alanine dipeptide in water." Journal of the American Chemical Society. 2004 Mar 3; 126(8):2574-81.
2003 Dec 17
Grossfield A, Ren P, Ponder JW. "Ion solvation thermodynamics from simulation with a polarizable force field." Journal of the American Chemical Society. 2003 Dec 17; 125(50):15671-82.
2000 Nov 1
Grossfield A, Sachs J, Woolf TB. "Dipole lattice membrane model for protein calculations." Proteins. 2000 Nov 1; 41(2):211-23.
2000 Sep 22
Petrache HI, Grossfield A, MacKenzie KR, Engelman DM, Woolf TB. "Modulation of glycophorin A transmembrane helix interactions by lipid bilayers: molecular dynamics calculations." Journal of molecular biology. 2000 Sep 22; 302(3):727-46.
2000 Feb
Woolf TB, Grossfield A, Tychko M. "Differences between apo and three holo forms of the intestinal fatty acid binding protein seen by molecular dynamics computer calculations." Biophysical journal. 2000 Feb; 78(2):608-25.