Presentation Skills Workshop

Journal Articles

  1. Poruthoor, A. J, Sharma, A., and Grossfield, A. Understanding the free-energy landscape of phase separation in lipid bilayers using molecular dynamics. Biophysical J. (2023), 122, 1-16, (pdf)
  2. Seckler, J. M., Robinson, E. N., Lewis, S. J. & Grossfield, A. Surveying nonvisual arrestins reveals allosteric interactions between functional sites. Proteins Struct Funct Bioinform (2022) doi:10.1002/prot.26413, (pdf)
  3. Sreyoshi Sur and Alan Grossfield, “Effects of cholesterol on the mechanism of fengycin, a biofungicide“, Biophysical Journal, 2022, 121, 1-12, (pdf)
  4. Onukwufor, John O., Farooqi, M. Arsalan, Vodičková, Anežka, Koren, Shon,  A, Baldzizhar, Aksana, Berry, Brandon, J. Beutner, Gisela, Porter, George A., Belousov, Vsevolod, Grossfield, Alan, Wojtovich, Andrew P., “A reversible mitochondrial complex I thiol switch mediates hypoxic avoidance behavior in C. elegans“, Nature Communications, 2022, 13, 2403, (pdf)
  5. Benjamin GastonSanthosh M Baby Walter J MayAlex P YoungAlan GrossfieldJames N BatesJames M Seckler Christopher G WilsonStephen J Lewis, “D-Cystine di(m)ethyl ester reverses the deleterious effects of morphine on ventilation and arterial blood gas chemistry while promoting antinociception“, Scientific Reports, 2021, 11;11(1):10038, (pdf)
  6. Grossfield, A., “How to be a good member of a scientific software community“, Living J. Comp. Mol.  Sci.,, 2022 (pdf
  7. Romo, T. D., Grossfield, A., and Markelz, A.G., “Persistent Protein Motions in a Rugged Energy Landscape Revealed by Normal Mode Ensemble Analysis“, J. Chem. Inf. Model, 2020, (pdf)
  8. Maji, D., Grossfield, A., and Kielkopf, C. L., “Structures of SF3b1 reveal a dynamic Achilles heel of spliceosome assembly: Implications for cancer-associated abnormalities and drug discovery“, BBA Gene Regulatory Mechanisms, 2019, 1862, 194440, (pdf)
  9. Smith, L. G., Tan, Z., Spasic, A., Dutta, D., Salas-Estrada, L. A., Grossfield, A., and Mathews, D. H., “Chemically accurate relative folding stability of RNA hairpins from molecular simulations“, J. Chem. Theor. Comput., 2018, 14, 6598-6612, (pdf)
  10. Grossfield, A., Patrone, P. N., Roe, D. R., Schultz, A. J., Siderius, D. W., and Zuckerman, D. M., “Best practices for quantification of uncertainty and sampling quality in molecular simulations“, Living Journal of Computational Molecular Science, 2018, 1, 1-24, (pdf)
  11. Sur, S., Romo, T. D., and Grossfield, A., “Selectivity and mechanism of fengycin, an antimicrobial lipopeptide, from molecular dynamics“, J. Phys. Chem. B, 2018, 122, 2219-2226, (pdf)
  12. Salas-Estrada, L. A., Leioatts, N., Romo, T. D., and Grossfield, A., “Lipids Alter Rhodopsin Function via Ligand-like and Solvent-like Interactions“, Biophys. J., 2018, 114, 355-367, (pdf)
  13. Thompson, J. L., Zhao, Y., Stathopulos, P. B., Grossfield, A., and Shuttleworth, T. J.,”Phosphorylation-mediated structural changes within the SOAR domain of STIM1 enable specific activation of distinct Orai channels“,  J. Biol. Chem., 2018
  14. Romo, T. D., Lewis, A. K., Braun. A. R., Grossfield, A., and Sachs, J. N., “Minimal Nucleation State of α‐Synuclein Is Stabilized by Dynamic Threonine−Water Networks“, ACS Chemical Neuroscience, 8, 2017, 1859-1864, (pdf)
  15. Aytenfisu, A. H., Spasic, A., Grossfield, A., Stern, H. A., Mathews, D. H., “Revised RNA dihedral parameters for the Amber force field improve RNA molecular dynamics“, J. Chem. Theor. Comput., 13, 2017, 900-915, (pdf)
  16. Lin, D., “Generalized and efficient algorithm for computing multipole energies and gradients based on cartesian tensors“, J. Chem. Phys., 143, 2015, 114115, (pdf)
  17. Lin, D. and Grossfield, A., “Thermodynamics of micelle formation and membrane fusion modulate antimicrobial lipopeptide activity“, Biophysical Journal, 2015, 109, 750-759, (pdf)
  18. Leioatts, N., Romo, T. D., Danial, S. A., and Grossfield, A., “Retinal conformation changes rhodopsin’s dynamic ensemble“, Biophysical Journal, 2015, 109, 608-617, (pdf)
  19. Romo, T. D., Leioatts, N. and Grossfield, A., “Lightweight Object Oriented Structure Analysis: Tools for building tools to analyze molecular dynamics simulations“, J. Comput. Chem., 2014, 35, 2305-2318, (pdf)
  20. Lin, D. and Grossfield, A., “Thermodynamics of Antimicrobial Lipopeptide Binding to Membranes: Origins of Affinity and Selectivity“, Biophysical Journal, 2014, 107, 1862-1872, (pdf)
  21. Romo, T. D. and Grossfield, A., “How fast is your camera? Time scales for molecular motion and their role in restraining molecular dynamics“, Biophysical Journal, 2014, 106, 2549-2551, (pdf)
  22. Leioatts, N., Suresh, P., Romo, T. D., and Grossfield, A., “Structure-based simulations reveal concerted dynamics of GPCR activation“, Proteins, 2014, 82, 2538-2551 (pdf)
  23. Mnpotra, J.S., Qiao, Z., Cai, J., Lynch, D. L., Grossfield, A., Leioatts, N., Hurst, D. P., Pitman, M. C., Song, Z.-H., Reggio, P.H., “Structural basis of G protein-coupled receptor-Gi protein interaction: formation of the cannabinoid CB2 Receptor/Gi Protein Complex“, J. Biol. Chem., 2014, 289, 20259-20272
  24. Romo, T. D. and Grossfield, A., “Unknown Unknowns: the Challenge of Systematic and Statistical Error in Molecular Dynamics Simulations“, Biophysical Journal, 2014, 106, 1553-1554, (pdf)
  25. Leioatts, N., Mertz, B., Martinez-Mayorga, K., Romo, T. D., Pitman, M. C., Feller, S. E., Grossfield, A., Brown, M. F., “Retinal ligand mobility explains internal hydration and reconciles active rhodopsin structures“, Biochemistry,  2014, 53, pp 376–385(pdf)
  26. Kimura, T., Vukoti, K., Lynch, D. L., Hurst, D. P, Grossfield, A., Pitman, M. C., Reggio, P. H., Yeliseev, A. A., Gawrisch, K., “Global fold of human cannabinoid type 2 receptor probed by solid-state 13C-, 15N-MAS NMR and molecular dynamics simulations“, Proteins: Struc. Func. Bioinf., 2013, 82, 452-465 (pdf)
  27. Horn, J. N., Cravens, A. and Grossfield, A., “Interactions between fengycin and model bilayers quantified by coarse-grained molecular dynamics“, Biophysical Journal, 2013, 105, 1612-1623, (pdf)
  28. Horn, J. N., Romo, T. D., and Grossfield, A., “Simulating the mechanism of antimicrobial lipopeptides with all-atom molecular dynamics”, Biochemistry, 2013, 52,  5604-5610, (pdf)
  29. Leioatts, N., and Grossfield, A., “Molecular dynamics simulations of membranes and membrane proteins“, in Molecular modeling at the atomic scale – Methods and applications in quantitative biology, ed. Ruhong Zhou, CRC Press, 2014, Ch 9, 243-270
  30. Seckler, J. M., Leioatts, N., Miao, H., and Grossfield, A. “The interplay of structure and dynamics in the function of HIV-1 reverse transcriptase”, Proteins: Struc. Func. Bioinf., 2013, 81, 1792-1801, (pdf)
  31. Horn, J. N., Kao, T.-C., and Grossfield, A., “Coarse-grained molecular dynamics provides insight into the interactions of lipids and cholesterol with rhodopsin”, in G Protein-Coupled Receptor –  Modeling and Simulation, ed. Marta Filizola, Springer,  Adv. Exp. Med. Biol., 2014, 796:75–94 (pdf)
  32. Leioatts, N., Romo, T. D., and Grossfield, A., “Elastic network models are robust to variations in formalism“, J. Chem. Theor. Comput., 2012, 8,  2424-2434 (pdf)
  33. Olausson, B., Grossfield, A., Pitman, M., Brown, M., Feller, S., Vogel, A., Molecular dynamics simulations reveal specific interactions of post-translational palmitoyl modifications with rhodopsin in membranes, J. Am. Chem. Soc., 2012, 134, 4234-4331 (pdf)
  34. Horn, J. N., Sengillo, J. D., Lin, D., Romo, T. D., and Grossfield, A., Characterization of a potent antimicrobial lipopeptide via coarse-grained molecular dynamics, Biochim. Biophys. Acta, 2012, 1818, 212-218 (pdf)
  35. Romo, T. D., and Grossfield, A. Block covariance overlap method and convergence in molecular dynamics simulation, J. Chem. Theor. Comput., 2011, 7, 2464-2472 (pdf)
  36. Romo, T. D., Bradney, L. A., Greathouse, D. V., and Grossfield, A. Membrane binding of an acyl-lactoferricin B antimicrobial peptide from solid-state NMR experiments and molecular dynamics simulations, Biochim. Biophys. Acta, 2011, 1808, 2019-2030 (pdf)
  37. Grossfield, A., Recent progress in the study of G protein-coupled receptors with molecular dynamics computer simulations, Biochim. Biophys. Acta, 2011, 1808, 1868–1878, (pdf)
  38. Romo, T. D. and Grossfield, A., Validating and improving elastic network models using molecular dynamics simulations, Proteins, 2011, 79, 23-34 (pdf)
  39. Hurst, D. P., Grossfield, A., Lynch, D. L., Feller, S., Romo, T. D., Gawrisch, K., Pitman, M. C., and Reggio, P. H., A lipid pathway for ligand binding is necessary for a cannabinoid G protein-coupled receptor, J. Biol. Chem., 2010, 285, 17954-17964, PMID: 20220143 (pdf)
  40. Romo, T. D., Grossfield A., and Pitman, M. C. Concerted Interconversion Between Ionic Lock Substates of the b2-Adrenergic Receptor Revealed by Microsecond Time Scale Molecular Dynamics, Biophysical Journal, 2010, 98, 76-84 (pdf)
  41. Romo, T. D. and Grossfield A., LOOS: An Extensible Platform for the Structural Analysis of Simulations, Proceedings of 31st IEEE-Engineering in Medicine and Biology Conference (2009), 2332-2335 (pdf)
  42. Grossfield, A., and Zuckerman, D. M. Quantifying uncertainty and sampling quality in biomolecular simulations, Annual Reports in Computational Chemistry, 2009, 5, 23-48, PMC2865156 (pdf)
  43. Khelashvili, G., Grossfield, A., Feller, S. E., Pitman, M. C., and Weinstein, H. Structural and dynamic effects of cholesterol at preferred sites of interaction with rhodopsin identified from microsecond length molecular dynamics simulations, Proteins: Struc. Func. Bioinf., 2009, 76, 403-417 (pdf)
  44. Grossfield, A. Implicit modeling of membranes, in “Computational Modeling of Membranes”, ed Scott Feller, Current Topics in Membranes 2008, 60, 131-157 (pdf)
  45. Grossfield, A., Pitman, M. C., Feller, S. E., Soubias, O., and Gawrisch, K. Internal Hydration Increases during Activation of the G-Protein-Coupled Receptor Rhodopsin, J. Mol. Biol. 2008, 381, 478-486 (pdf)
  46. Lau, P.-W., Grossfield, A., Feller, S. E., Pitman, M. C., Brown, M. F. Dynamic structure of retinal inverse agonist of rhodopsin probed by molecular dynamics, J. Mol. Biol. 2007, 372, 906-917 (pdf)
  47. O’Neil, L. L., Grossfield, A., Wiest, O. Computational Investigation of the Base Flipping of the Thymine Dimer in Duplex DNA, J. Phys. Chem. B, 2007, 111, 11843-11849 (pdf)
  48. Grossfield, A., Feller, S. E., Pitman, M. C. Convergence of molecular dynamics simulations of membrane proteins, Proteins: Struc. Func. Bioinf., 2007, 67, 31-40 (pdf)
  49. Martínez-Mayorga, K., Pitman, M. C., Grossfield, A., Feller, S. E., and Brown, M. F. Retinal counterion switch mechanism in vision evaluated by molecular simulation, J. Am. Chem. Soc., 2006, 128, 16502-16503 (pdf)
  50. 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, 18553-18559 (pdf)
  51. 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, 8907-8909 (pdf)
  52. Grossfield, A., Feller, S. E., Pitman, M. C., A role for direct interactions in the modulation of rhodopsin by omega-3 polyunsaturated lipids, Proc. Nat. Acad. Sci. USA, 2006, 103, 4888-4893 (pdf)
  53. Fitch, B. G., Rayshubskiy, A., Eleftheriou, M, Ward, T.J.C., Giampapa, M., Zhestkov, Y., Pitman, M. C., Suits, F., Grossfield, A., Pitera, J., Swope, W., Zhou, R., Feller, S., and Germain. R. S., Blue Matter: Strong scaling of molecular dynamics on Blue Gene/L. In V. Alexandrov, D. van Albada, P. Sloot, and J. Dongarra, editors, International Conference on Computational Science (ICCS 2006), volume 3992 of LNCS, pages 846–854. Springer-Verlag, 2006.
  54. Pitman, M. C., Grossfield, A., Suits, F. and Feller, S. E., Role of cholesterol and polyunsaturated lipids in lipid-protein interaction: molecular dynamics simulations of rhodopsin in a realistic membrane environment, J. Am. Chem. Soc., 2005, 127, 4576-4577 (pdf)
  55. Fitch, B. G., Rayshubskiy, A., Eleftheriou, M, Ward, T.J.C., Giampapa, M., Zhestkov, Y., Pitman, M. C., Suits, F., Grossfield, A., Pitera, J., Swope, W., Zhou, R., Feller, S., and Germain. R. S., Blue Matter: Strong scaling of molecular dynamics on Blue Gene/L. Research Report RC23688, IBM Research Division, 2005.
  56. Grossfield, A. Dependence of ion hydration on the sign of the ion’s charge, J. Chem. Phys., 2005, 122, 024506-10 (pdf)
  57. Drozdov, A. N., Grossfield, A., and Pappu, R. V., The role of solvent in determining conformational preferences of alanine dipeptide in water, J. Am. Chem. Soc., 2004, 126, 2574-2581 (pdf)
  58. Grossfield, A., Ren, P., and Ponder, J. W., Single ion solvation thermodynamics from simulations with a polarizable force field, J. Am. Chem. Soc., 2003, 125, 14