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 42 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 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 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.
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 35(32):2305-18. Epub 2014 Oct 18.
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 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.
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. Link
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.
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. Link
Grossfield, A.; Feller, S. E.; Pitman, M. C.;. "Convergence of molecular dynamics simulations of membrane proteins". Proteins. 2007; 67(31): 31-40. Link
O'Neil L, L.; Grossfield, A.; Wiest, O.;. "Base Flipping of the Thymine Dimer in Duplex DNA". J Phys Chem B. 2007; . Link
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. Link
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. Link
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. Link
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. Link
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. Link
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. Link
Grossfield, A.;. "Dependence of ion hydration on the sign of the ion's charge". J Chem Phys. 2005; 122(32): 024506. Link
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. Link
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. Link
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. Link
Grossfield, A.; Sachs, J.; Woolf, T. B.;. "Dipole lattice membrane model for protein calculations". Proteins. 2000; 41(32): 211-23. Link
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. Link