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    Andrew Pohorille, PhD, MS

    TitleProfessor
    SchoolUCSF School of Pharmacy
    DepartmentPharmaceutical Chemistry
    Address3333 California Street
    San Francisco CA 94104
    Phone650-604-5759
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      Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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      1. Wei C, Pohorille A. M2 proton channel: toward a model of a primitive proton pump. Orig Life Evol Biosph. 2015 Jun; 45(1-2):241-8. PMID: 25777465.
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      2. A Wilson M, Wei C, Pohorille A. Towards co-evolution of membrane proteins and metabolism. Orig Life Evol Biosph. 2014 Dec; 44(4):357-61. PMID: 25614291.
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      3. Saha R, Pohorille A, Chen IA. Molecular crowding and early evolution. Orig Life Evol Biosph. 2014 Dec; 44(4):319-24. PMID: 25585804.
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      4. Wilson MA, Nguyen TH, Pohorille A. Combining molecular dynamics and an electrodiffusion model to calculate ion channel conductance. J Chem Phys. 2014 Dec 14; 141(22):22D519. PMID: 25494790.
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      5. Wei C, Pohorille A. Flip-flop of oleic acid in a phospholipid membrane: rate and mechanism. J Phys Chem B. 2014 Nov 13; 118(45):12919-26. PMID: 25319959.
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      6. Comer J, Gumbart JC, Hénin J, Lelièvre T, Pohorille A, Chipot C. The adaptive biasing force method: everything you always wanted to know but were afraid to ask. J Phys Chem B. 2015 Jan 22; 119(3):1129-51. PMID: 25247823; PMCID: PMC4306294.
      7. Wei C, Pohorille A. Activation and proton transport mechanism in influenza A M2 channel. Biophys J. 2013 Nov 5; 105(9):2036-45. PMID: 24209848; PMCID: PMC3824548.
      8. Wei C, Pohorille A. Permeation of aldopentoses and nucleosides through fatty acid and phospholipid membranes: implications to the origins of life. Astrobiology. 2013 Feb; 13(2):177-88. PMID: 23397957.
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      9. Pohorille A. Processes that drove the transition from chemistry to biology: concepts and evidence. Orig Life Evol Biosph. 2012 Oct; 42(5):429-32. PMID: 23080008.
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      10. Pohorille A, Pratt LR. Is water the universal solvent for life? Orig Life Evol Biosph. 2012 Oct; 42(5):405-9. PMID: 23065397.
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      11. Wilson MA, Wei C, Bjelkmar P, Wallace BA, Pohorille A. Molecular dynamics simulation of the antiamoebin ion channel: linking structure and conductance. Biophys J. 2011 May 18; 100(10):2394-402. PMID: 21575573; PMCID: PMC3093558.
      12. Wei C, Pohorille A. Permeation of nucleosides through lipid bilayers. J Phys Chem B. 2011 Apr 7; 115(13):3681-8. PMID: 21405137.
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      13. Pohorille A, Jarzynski C, Chipot C. Good practices in free-energy calculations. J Phys Chem B. 2010 Aug 19; 114(32):10235-53. PMID: 20701361.
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      14. Wei C, Pohorille A. Permeation of membranes by ribose and its diastereomers. J Am Chem Soc. 2009 Jul 29; 131(29):10237-45. PMID: 19621967.
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      15. Pohorille A, Deamer D. Self-assembly and function of primitive cell membranes. Res Microbiol. 2009 Sep; 160(7):449-56. PMID: 19580865.
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      16. Reysenbach AL, Hamamura N, Podar M, Griffiths E, Ferreira S, Hochstein R, Heidelberg J, Johnson J, Mead D, Pohorille A, Sarmiento M, Schweighofer K, Seshadri R, Voytek MA. Complete and draft genome sequences of six members of the Aquificales. J Bacteriol. 2009 Mar; 191(6):1992-3. PMID: 19136599; PMCID: PMC2648382.
      17. Des Marais DJ, Nuth JA, Allamandola LJ, Boss AP, Farmer JD, Hoehler TM, Jakosky BM, Meadows VS, Pohorille A, Runnegar B, Spormann AM. The NASA Astrobiology Roadmap. Astrobiology. 2008 Aug; 8(4):715-30. PMID: 18793098.
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      18. Darve E, Rodríguez-Gómez D, Pohorille A. Adaptive biasing force method for scalar and vector free energy calculations. J Chem Phys. 2008 Apr 14; 128(14):144120. PMID: 18412436.
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      19. Langley P, Shiran O, Shrager J, Todorovski L, Pohorille A. Constructing explanatory process models from biological data and knowledge. Artif Intell Med. 2006 Jul; 37(3):191-201. PMID: 16781850.
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      20. Hénin J, Pohorille A, Chipot C. Insights into the recognition and association of transmembrane alpha-helices. The free energy of alpha-helix dimerization in glycophorin A. J Am Chem Soc. 2005 Jun 15; 127(23):8478-84. PMID: 15941282.
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      21. Pohorille A, Schweighofer K, Wilson MA. The origin and early evolution of membrane channels. Astrobiology. 2005 Feb; 5(1):1-17. PMID: 15711166.
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      22. Rodriguez-Gomez D, Darve E, Pohorille A. Assessing the efficiency of free energy calculation methods. J Chem Phys. 2004 Feb 22; 120(8):3563-78. PMID: 15268518.
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      23. Bay SD, Chrisman L, Pohorille A, Shrager J. Temporal aggregation bias and inference of causal regulatory networks. J Comput Biol. 2004; 11(5):971-85. PMID: 15700412.
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      24. Pohorille A, Wilson MA, Chipot C. Membrane peptides and their role in protobiological evolution. Orig Life Evol Biosph. 2003 Apr; 33(2):173-97. PMID: 12967266.
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      25. Chrisman L, Langley P, Bay S, Pohorille A. Incorporating biological knowledge into evaluation of causal regulatory hypotheses. Pac Symp Biocomput. 2003; 128-39. PMID: 12603023.
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      26. Bay SD, Shrager J, Pohorille A, Langley P. Revising regulatory networks: from expression data to linear causal models. J Biomed Inform. 2002 Oct-Dec; 35(5-6):289-97. PMID: 12968777.
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      27. Pratt LR, Pohorille A. Hydrophobic effects and modeling of biophysical aqueous solution interfaces. Chem Rev. 2002 Aug; 102(8):2671-92. PMID: 12175264.
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      28. Pohorille A, Deamer D. Artificial cells: prospects for biotechnology. Trends Biotechnol. 2002 Mar; 20(3):123-8. PMID: 11841864.
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      29. Shrager J, Langley P, Pohorille A. Guiding revision of regulatory models with expression data. Pac Symp Biocomput. 2002; 486-97. PMID: 11928501.
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      30. Parusel AB, Pohorille A. A semiempirical study of the optimized ground and excited state potential energy surfaces of retinal and its protonated Schiff base. J Photochem Photobiol B. 2001 Dec 1; 65(1):13-21. PMID: 11748000.
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      31. Lanyi JK, Pohorille A. Proton pumps: mechanism of action and applications. Trends Biotechnol. 2001 Apr; 19(4):140-4. PMID: 11250031.
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      32. Sokolowska J, Pohorille A. Models of risk and choice: challenge or danger. Acta Psychol (Amst). 2000 Jun; 104(3):339-69. PMID: 10900700.
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      33. Schweighofer KJ, Pohorille A. Computer simulation of ion channel gating: the M(2) channel of influenza A virus in a lipid bilayer. Biophys J. 2000 Jan; 78(1):150-63. PMID: 10620282; PMCID: PMC1300626.
      34. Chipot C, Maigret B, Pohorille A. Early events in the folding of an amphipathic peptide: A multinanosecond molecular dynamics study. Proteins. 1999 Sep 1; 36(4):383-99. PMID: 10450080.
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      35. Eger EI, Halsey MJ, Harris RA, Koblin DD, Pohorille A, Sewell JC, Sonner JM, Trudell JR. Hypothesis: volatile anesthetics produce immobility by acting on two sites approximately five carbon atoms apart. Anesth Analg. 1999 Jun; 88(6):1395-400. PMID: 10357351.
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      36. Eger EI, Ionescu P, Laster MJ, Gong D, Hudlicky T, Kendig JJ, Harris RA, Trudell JR, Pohorille A. Minimum alveolar anesthetic concentration of fluorinated alkanols in rats: relevance to theories of narcosis. Anesth Analg. 1999 Apr; 88(4):867-76. PMID: 10195540.
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      37. Pickel VM, Pohorille A, Chan J, Tate SS, Nirenberg MJ. Regional and subcellular distribution of a neutral and basic amino acid transporter in forebrain neurons containing nitric oxide synthase. J Comp Neurol. 1999 Feb 22; 404(4):459-72. PMID: 9987991.
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      38. Chipot C, Pohorille A. Folding and translocation of the undecamer of poly-L-leucine across the water-hexane interface. A molecular dynamics study. J Am Chem Soc. 1998 Nov 25; 120(46):11912-24. PMID: 11542762.
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      39. Pohorille A, Wilson MA, New MH, Chipot C. Concentrations of anesthetics across the water-membrane interface; the Meyer-Overton hypothesis revisited. Toxicol Lett. 1998 Nov 23; 100-101:421-30. PMID: 10049175.
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      40. Bellocchio EE, Hu H, Pohorille A, Chan J, Pickel VM, Edwards RH. The localization of the brain-specific inorganic phosphate transporter suggests a specific presynaptic role in glutamatergic transmission. J Neurosci. 1998 Nov 1; 18(21):8648-59. PMID: 9786972.
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      41. Pohorille A. Transient cavities in liquids and the nature of the hydrophobic effect. Pol J Chem. 1998 Jul; 72(7):1680-90. PMID: 11542255.
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      42. Chipot C, Pohorille A. Conformational equilibria of terminally blocked single amino acids at the water-hexane interface. A molecular dynamics study. J Phys Chem B. 1998 Jan 1; 102(1):281-90. PMID: 11541119.
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      43. Nirenberg MJ, Chan J, Pohorille A, Vaughan RA, Uhl GR, Kuhar MJ, Pickel VM. The dopamine transporter: comparative ultrastructure of dopaminergic axons in limbic and motor compartments of the nucleus accumbens. J Neurosci. 1997 Sep 15; 17(18):6899-907. PMID: 9278525.
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      44. Wilson MA, Pohorille A. Adsorption and solvation of ethanol at the water liquid-vapor interface: a molecular dynamics study. J Phys Chem B. 1997 Apr 17; 101(16):3130-5. PMID: 11540504.
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      45. Eger EI, Koblin DD, Harris RA, Kendig JJ, Pohorille A, Halsey MJ, Trudell JR. Hypothesis: inhaled anesthetics produce immobility and amnesia by different mechanisms at different sites. Anesth Analg. 1997 Apr; 84(4):915-8. PMID: 9085981.
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      46. Chipot C, Wilson MA, Pohorille A. Interactions of anesthetics with the water-hexane interface. A molecular dynamics study. J Phys Chem B. 1997 Jan 30; 101(5):782-91. PMID: 11542402.
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      47. Hummer G, Garde S, García AE, Pohorille A, Pratt LR. An information theory model of hydrophobic interactions. Proc Natl Acad Sci U S A. 1996 Aug 20; 93(17):8951-5. PMID: 11607700; PMCID: PMC38575.
      48. Wilson MA, Pohorille A. Mechanism of unassisted ion transport across membrane bilayers. J Am Chem Soc. 1996 Jul 17; 118(28):6580-7. PMID: 11539569.
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      49. Pohorille A, Cieplak P, Wilson MA. Interactions of anesthetics with the membrane-water interface. Chem Phys. 1996 Apr 1; 204(2-3):337-45. PMID: 11540160.
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      50. Pohorille A, Wilson MA. Excess chemical potential of small solutes across water--membrane and water--hexane interfaces. J Chem Phys. 1996 Mar 8; 104(10):3760-73. PMID: 11539401.
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      51. Pohorille A, Chipot C, New MH, Wilson MA. Molecular modeling of protocellular functions. Pac Symp Biocomput. 1996; 550-69. PMID: 9390258.
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      52. Benjamin I, Wilson MA, Pohorille A, Nathanson GM. Scattering of water from the glycerol liquid-vacuum interface. Chem Phys Lett. 1995 Sep 15; 243(3-4):222-8. PMID: 11540427.
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      53. Pohorille A, Wilson MA. Molecular dynamics studies of simple membrane-water interfaces: structure and functions in the beginnings of cellular life. Orig Life Evol Biosph. 1995 Jun; 25(1-3):21-46. PMID: 11536672.
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      54. Wilson MA, Pohorille A, Jenniskens P, Blake DF. Probing the structure of cometary ice. Orig Life Evol Biosph. 1995 Jun; 25(1-3):3-19. PMID: 11536679.
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      55. Wilson MA, Pohorille A. Molecular dynamics of a water-lipid bilayer interface. J Am Chem Soc. 1994; 116(4):1490-501. PMID: 11543595.
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      56. Benjamin I, Pohorille A. Isomerization reaction dynamics and equilibrium at the liquid-vapor interface of water. A molecular-dynamics study. J Chem Phys. 1993 Jan 1; 98(1):236-42. PMID: 11539443.
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      57. Pohorille A, Benjamin I. Structure and Energetics of model amphiphilic molecules at the water liquid-vapor interface. A molecular dynamics study. J Phys Chem. 1993; 97(11):2664-70. PMID: 11539476.
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      58. Pohorille A, Wilson MA. Viewpoint 9--molecular structure of aqueous interfaces. J Mol Struct. 1993; 284:271-98. PMID: 11539444.
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      59. Pratt LR, Pohorille A. Theory of hydrophobicity: transient cavities in molecular liquids. Proc Natl Acad Sci U S A. 1992 Apr; 89:2995-9. PMID: 11537863; PMCID: PMC48790.
      60. Wilson MA, Pohorille A. Interaction of monovalent ions with the water liquid-vapor interface: a molecular dynamics study. J Chem Phys. 1991 Oct 15; 95(8):6005-13. PMID: 11538294.
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      61. Pohorille A, Benjamin I. Molecular dynamics of phenol at the liquid-vapor interface of water. J Chem Phys. 1991 Apr 15; 94(8):5599-605. PMID: 11540075.
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      62. Pohorille A, Ross WS, Tinoco I. DNA dynamics in aqueous solution: opening the double helix. Int J Supercomput Appl. 1990; 4(3):81-96. PMID: 11538365.
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      63. Pohorille A, Pratt LR. Cavities in molecular liquids and the theory of hydrophobic solubilities. J Am Chem Soc. 1990; 112(13):5066-74. PMID: 11540917.
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      64. Wilson MA, Pohorille A, Pratt LR. Comment on "Study on the liquid-vapor interface of water. I. Simulation results of thermodynamic properties and orientational structure". J Chem Phys. 1989 May 1; 90(9):5211-3. PMID: 11542468.
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      65. Wilson MA, Pohorille A, Pratt LR. Interaction of a sodium ion with the water liquid-vapor interface. Chem Phys. 1989; 129:209-12. PMID: 11542383.
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      66. Wilson MA, Pohorille A, Pratt LR. Surface potential of the water liquid-vapor interface. J Chem Phys. 1988 Mar 1; 88(5):3281-5. PMID: 11542143.
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      67. Owenson B, MacElroy RD, Pohorille A. Molecular dynamics study of ion capture from water by a model ionophore, tetraprotonated cryptand SC24. J Am Chem Soc. 1988; 110(21):6992-7000. PMID: 11542140.
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      68. Owenson B, MacElroy RD, Pohorille A. A molecular dynamics study of chloride binding by the cryptand SC24. J Mol Struct. 1988; 179:467-84. PMID: 11542142.
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      69. Pohorille A, Pratt LR, LaViolette RA, Wilson MA, MacElroy RD. Comparison of the structure of harmonic aqueous glasses and liquid water. J Chem Phys. 1987 Nov 15; 87(10):6070-7. PMID: 11542382.
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      70. Wilson MA, Pohorille A, Pratt LR. Molecular dynamics of the water liquid-vapor interface. J Phys Chem. 1987; 91(19):4873-8. PMID: 11539733.
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      71. Pohorille A, Pratt LR. Theoretical methods for obtaining free energies of biomolecular equilibria in aqueous solutions. Methods Enzymol. 1986; 127:64-78. PMID: 3736431.
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      72. Pohorille A, Loew GH. Base-pairing properties of O-methylated bases of nucleic acids. Energetic and steric considerations. Biophys Chem. 1985 Jun; 22(1-2):37-51. PMID: 3896331.
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      73. Pohorille A, Pratt LR, Burt SK, MacElroy RD. Solution influence on biomolecular equilibria: nucleic acid base associations. J Biomol Struct Dyn. 1984 Mar; 1(5):1257-80. PMID: 6401105.
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      74. Pohorille A, Burt SK, MacElroy RD. Monte Carlo simulation of the influence of solvent on nucleic acid base associations. J Am Chem Soc. 1984; 106(2):402-9. PMID: 11541957.
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      75. Stolarski R, Pohorille A, Dudycz L, Shugar D. Comparison of theoretical and experimental approaches to determination of conformation of nucleosides about the glycosidic bond. Biochim Biophys Acta. 1980 Nov 14; 610(1):1-19. PMID: 6969094.
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      76. Pohorille A, Perahia D, Pullman B. Molecular orbital studies on the conformations of 8-amino- and 8-dimethylaminoadenosine 5'-monophosphate. Biochim Biophys Acta. 1978 Feb 16; 517(2):511-6. PMID: 626749.
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      77. Geller M, Pohorille A, Jaworski A. Electronic structure of thiouracils and their interaction with adenine. Biochim Biophys Acta. 1973 Nov 26; 331(1):1-8. PMID: 4761101.
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