1. Lin X, Li Z and Gorfe AA, "Reversibility of the effects of peptide concentration and lipid composition on the clustering of H-Ras lipid anchors", Biophysical Journal, 2015, In press.
  2. Prakash P, Sayyed-Ahmad A and Gorfe AA, "pMD-membrane: A method for ligand binding site identification in membrane-bound proteins", PLoS Comput Biol, 2015, 11(10): e1004469.
  3. McCarthy M, Prakash P and Gorfe AA "Computational allosteric ligand binding site identification on Ras proteins", Acta Biochim Biophys Sin, 2015, 1–8.
  4. Prakash P, Hancock JF and Gorfe AA, "Binding hotspots on K-Ras: Consensus ligand binding sites and other reactive regions from probe-based molecular dynamics analysis", Proteins 2015, 83(5): 898-909.
  5. Li Z and Gorfe AA, "Receptor-mediated membrane adhesion of lipid-polymer hybrid (LPH) nanoparticles studied by dissipative particle dynamics simulations", Nanoscale, 2015, 7, 814-824.
  6. Li Z and Gorfe AA, "Modulation of a Small Two-Domain Lipid Vesicle by Linactants", Journal of Physical Chemistry B, 2014, 18(30): 9028-9036.
  7. Li H and Gorfe AA, "Membrane Remodeling by Surface-Bound Protein Aggregates: Insights from Coarse-Grained Molecular Dynamics Simulation", The Journal of Physical Chemistry Letters, 2014, 5(8): 1457-1462.
  8. Prakash P and Gorfe AA, "Overview of simulation studeis on the enzymatic activity and conformational dynamics of the GTPase Ras", Molecular Simulation, 2014, 40(10-11): 839-847.
  9. Hocker HJ, Maharaj N and Gorfe AA, "LIBSA - Method for the determination of ligand-binding preference to allosteric sites on receptor ensembles", Journal of Chemical Information and Modeling, 2014, 24;54(2):530-538.
  10. Ramaswamy SS, Maclean DM, Gorfe AA, Jayaraman V, "Proton mediated conformational changes in an Acid Sensing Ion Channel", Journal of Biological Chemistry, 2013, 288(50): 35896-35905.
  11. Li Z and Gorfe AA, "Deformation of a Two-domain Lipid Bilayer due to Asymmetric Insertion of Lipid-modified Ras Peptides", Soft Matter, 2013, 9: 11249-11256.
  12. Prakash P and Gorfe AA, "Phosphatidylcholine attenuates aggregation of non-steroidal anti-inflammatory drugs with bile acids", Biochemistry, 2013, 52(42): 7461–7469.
  13. Brand CS, Hocker HJ, Gorfe AA, Cavasotto CN, and Dessauer CW, "Isoform Selectivity of Adenylyl Cyclase Inhibitors: Characterization of Known and Novel Compounds", Journal of Pharmacology and Experimental Therapeutics, 2013, 347(2):265-275.
  14. Li H and Gorfe AA, "Aggregation of lipid-anchored full-length H-Ras in lipid bilayers: Simulations with the MARTINI force field", PLoS ONE, 2013, 8(7):e71018.
  15. Prakash P and Gorfe AA, "Lessons from computer simulations of Ras proteins in solution and in membrane", BBA-General Subjects, 2013, 1830(110): 5211-5218.
  16. Hocker JH, Kwang-Jin C, Chung-Ying KC, Rambahal N, Sagineedu SR, Shaari K, Stanslas J, Hancock JF, Gorfe AA, "Andrographolide derivatives inhibit guanine nucleotide exchange and abrogate oncogenic Ras function", Proceedings of the National Academy of Sciences USA, 2013, 110(25):10201-10206.
  17. Cho KJ, Park JH, Piggot AM, Salim AA, Gorfe AA, Parton RG, Capon RJ, Lacey E and Hancock JF, "Staurosporines disrupt phosphatidylserine trafficking and mislocalize Ras proteins", Journal of Biological Chemistry, 2012: 287(52):43573-84.
  18. Li Z, Janosi L and Gorfe AA, "Formation and Domain-partitioning of H-ras Peptide Nanoclusters: Effects of Peptide Concentration and Lipid Composition", Journal of the American Chemical Society, 2012, 134(41):17278-85.
  19. Li Z and Gorfe AA, "What drives the clustering of membrane-bound Ras? (Commentary)", Small GTPases, 2012, 30;3(4): 244-247.
  20. Roach AN, Wang Z, Wu P, Zhang F, Chan R, Yonekubo Y, Paolo GD, Gorfe AA, Du G, "Phosphatidic acid regulation of PIPKI is critical for actin cytoskeletal reorganization", Journal of Lipid Research, 2012, 53(12): 2598-2609.
  21. Prakash P, Sayyed-Ahmad A, Zhou Y, Volk DE, Gorenstein DG, Dial EJ, Lichtenberger LM and Gorfe AA, "Aggregation Behavior of Ibuprofen, Cholic Acid and Dodecylphosphocholine Micelles", BBA-Biomembranes, 2012, 1818(12): 340-347.
  22. Janosi L, Li Z, Hancock JF and Gorfe AA, "Organization, Dynamics and Segregation of Ras Nanoclusters in Membrane Domains", Proceedings of the National Academy of Sciences USA, 2012, 109(21): 8097-102.
  23. Prakash P, Sayyed-Ahmad A and Gorfe AA,"The Role of Conserved Waters in Conformational Transitions of Q61H K-ras", PLoS Computational Biology, 2012, 8(2), e1002394.
  24. Gorfe AA and Hocker JH, "Membrane Targeting: Methods",eLS. John Wiley & Sons, Ltd: Chichester (2012).
  25. Grant BJ, Lukman S, Hocker H, Sayyah J, Heller Brown J, McCammon JA, Gorfe AA,"Novel Allosteric Sites on Ras for Lead Generation", PLoS ONE, 2011, 6, e25711.
  26. Durrant JD, Cao R, Gorfe AA, Zhu W, Li J, Sankovsky A, Oldfield E, McCammon JA, "Non-Bisphosphonate Inhibitors of Isoprenoid Biosynthesis Identified via Computer-Aided Drug Design",Chemical Biology and Drug Design, 2011, 78:323-32.
  27. Grant BJ, Gorfe AA, McCammon JA, "Large conformational changes in proteins: Signaling and other functions", Current Opinion in Structural Biology,2010, 20, 142-147.
  28. Zhou Y, Lu B-Z and Gorfe AA, "Continuum Electromechanical Modeling of Protein-Membrane Interaction", Physical Review E, 2010, 82: 041923-041928.
  29. Janosi L and Gorfe AA, "Segregation of negatively charged phospholipids by the polycationic and farnesylated membrane anchor of Kras", Biophysical Journal, 2010, 99:3666-3674.
  30. Grant JN, McCammon JA and Gorfe AA, "Conformational Selection in G-proteins: Lessons from Ras and Rho(Featured Article)", Biophysical Journal, 2010, 99:L87-L89.
  31. Gorfe AA, "Mechanisms of allostery and membrane attachment in Ras GTPases: Implications for anti-cancer drug discovery", Current Medicinal Chemistry, 2010, 17, 1-9.
  32. Janosi L and Gorfe AA, "Simulating POPC and POPC/POPG bilayers: Conserved packing and altered surface reactivity", Journal of Chemical Theory and Computation, 2010, 16:3267-3273.
  33. Janosi L and Gorfe AA, "Importance of the sphingosine base double bond geometry for the structural and thermodynamic properties of sphingomyelin bilayers(Featured Article)", Biophysical Journal, 2010, 99 (9):2957–2966.
  34. Lukman S, Grant B, Gorfe AA, Grant G and McCammon JA, "The distinct conformational dynamics of K-ras and H-ras A59G", PLoS Computational Biology 2010, 6:e1000922.
  35. Sayyed-Ahmad A, Lichtenberger LM and Gorfe AA, "Structure and Dynamics of Cholic Acid and Dodecylphosphocholine−Cholic Acid Aggregates", Langmuir, 2010, 26:13407-13414.
  36. Abankwa D, Gorfe AA, Inder K andHancock JF, "Membrane orientation and nanodomain organization generate Ras isoform diversity", Proceedings of the National Academy of Sciences USA, 2010, 107:1130-1135.
  37. Burke JE, Babakhani A,Gorfe AA,Kokotos G, Li S, Woods VL Jr, McCammon JA and Dennis EA, "Location of Inhibitors Bound to Group IVA Phospholipase A(2) Determined by Molecular Dynamics and Deuterium Exchange Mass Spectrometry", Journal of the American Chemical Society, 2009, 131:8083-91.
  38. Edreira MM, Li S, Wong S, Gorfe AA, Ribeiro-Neto F, Woods VL Jr, and Altschuler DL, "Phosphorylation-induced conformational change in Rap1B: Allosteric effects on switch domain and effector loop", Journal of Biological Chemistry, 2009, 284:27480-6
  39. Gorfe AA, Lu B-Z, Yu Z, and McCammon JA, "Enzyme activity versus structural dynamics: The case of acetylcholinesterase tetramer(Featured Article)", Biophysical Journal, 2009, 97:897-905.
  40. Khavrutskii I, Gorfe AA, Lu B-Z and McCammon JA, "Free energy for the permeation of Na+ and Cl- ions and their ion-pair through zwitterionic dimyristoyl phosphatidylcholine lipid bilayer by umbrella integration with harmonic fourier Beads", Journal of the American Chemical Society, 2009, 131:1706-16
  41. Grant B, Gorfe AA and McCammon JA, "Ras Conformational Switching: Simulating Nucleotide Dependent Conformational Transitions with Accelerated Molecular dynamics", PLoS Computational Biology, 2009, 5:e1000325.
  42. Gorfe AA and McCammon JA, "Similar membrane affinity of mono- and di-S-acylated Ras membrane anchors: A new twist in the role of protein lipidation", Journal of the American Chemical Society, 2008, 130, 12624-12625.
  43. Abankwa D, Gorfe AA, Hancock JF, "Mechanisms of Ras membrane organization and signalling: Ras on a rocker", Cell Cycle, 2008, 7, 2667-2673.
  44. Gorfe AA, Baron R and McCammon JA, "Water-membrane partition thermodynamics of an amphiphilic lipopeptide: An enthalpy driven hydrophobic effect", Biophysical Journal, 2008, 95, 3269-33277.
  45. Babkhani A, Gorfe AA, Kim J and McCammon JA, "Thermodynamics of peptide insertion and aggregation in a lipid bilayer", Journal of Physical Chemistry B, 2008, 112, 10528-10534.
  46. Gorfe AA, Grant B and McCammon JA, "Mapping the nucleotide and isoform dependent structural and dynamical features of Ras proteins", Structure, 2008, 16, 885-896.
  47. Abankwa D, Hanzal-Bayer M, Ariotti N, Plowman SJ, Gorfe AA, Parton RG, McCammon JA, Hancock JF, "A novel switch region regulates H-ras membrane orientation and signal output", The EMBO Journal, 2008, 27, 727-735.
  48. Gorfe AA, Chang CA, Ivanov I and McCammon JA, "Dynamics of the acetylcholinesterase tetramer", Biophysical Journal, 2008, 94,1144-1154.
  49. Abankwa D, Gorfe AA, Hancock JF, "Ras nanoclusters: Molecular structure and assembly (Review)", Seminars in Cell and Developmental Biology, 2007, 18, 599-607.
  50. Gorfe AA, Babakhani A and McCammon JA, "H-ras protein in a bilayer: Interaction and structure perturbation", Journal of the American Chemical Society, 2007, 129, 12280-12286.
  51. Gorfe AA, Babakhani A and McCammon JA, "Free Energy profile of H-ras membrane anchor upon membrane insertion", Angewadte Chemie International Edition, 2007, 46, 8234 - 8237.
  52. Gorfe AA and Caflisch A, "Ser170 controls the conformational multiplicity of the 166-175 loop in prion proteins: Implication for conversion and species barrier", FASEB Journal, 2007, 21,3279-3287.
  53. Babakhani A, Gorfe AA, Gullingsrud J, Kim J and McCammon JA, "Peptide insertion, positioning, and stabilization in a membrane: Insight from an all-atom molecular cynamics simulation", Biopolymers, 2007, 85:490-497
  54. Gorfe AA, Hanzal-Bayer M, Abankwa D, Hancock JF and McCammon JA, "Structure and dynamics of the full-length lipid-modified H-ras protein in complex with a DMPC bilayer", Journal of Medicinal Chemistry, 2007, 50:674-84
  55. Gorfe AA and Caflisch A, "Functional plasticity in the substrate binding site of beta-secretase (BACE)", Structure, 2005, 13:1487-1498.
  56. Gorfe AA, Pellarin R and Caflisch A, "Membrane localization and flexibility of a lipidated ras peptide studied by molecular dynamics simolations", Journal of the American Chemical Society, 2004, 126:15277-15286.
  57. Gorfe AA, Caflisch A, Jelesarov I, "The role of flexibility and hydration on the sequence-specific DNA recognition by the Tn916 integrase protein: a molecular dynamics analysis", Journal of Molecular Recognition, 2004, 17: 120-31
  58. Gorfe AA, Jelesarov I, "Energetics of sequence-specific protein-DNA association: Computational analysis of integrase Tn916 binding to its target DNA", Biochemistry, 2003, 42:11568-76
  59. Milev S, Gorfe AA, Karshikoff A, Clubb RT, Bosshard HR, Jelesarov I, "Energetics of sequence-specific protein-DNA association: Conformational stability of the DNA binding domain of integrase Tn916 and its cognate DNA duplex", Biochemistry, 2003, 42:3492-502.
  60. Milev S, Gorfe AA, Karshikoff A, Clubb RT, Bosshard HR, Jelesarov I, "Energetics of sequence-specific protein-DNA association: Binding of integrase Tn916 to its target DNA", Biochemistry, 2003, 42(12):3481-91.
  61. Phelan P, Gorfe AA, Jelesarov I, Marti DN, Warwicker J, Bosshard HR, "Salt bridges destabilize a leucine zipper designed for maximized ion pairing between helices", Biochemistry, 2002, 41:2998-3008.
  62. Gorfe AA, Ferrara P, Caflisch A, Marti DN, Bosshard HR, Jelesarov I, "Calculation of protein ionization equilibria with conformational sampling: pK(a) of a model leucine zipper, GCN4 and barnase",Proteins, 2002, 46:41-60.
  63. Gorfe AA, Brandsdal BO, Leiros HK, Helland R, Smalas AO, "Electrostatics of mesophilic and psychrophilic trypsin isoenzymes: Qualitative evaluation of electrostatic differences at the substrate binding site", Proteins, 2000, 40:207-17.