Publications

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PUBLICATIONS
  1. Turner, A.G., Honig, B., Parr, R.G. and Hoyland, J.R. (1964)
    Off-Center Hydrogen Atom Calculations.
    J. Chem. Phys. 40:3216-3220.
  2. Bradley, D.F., Lifson, S. and Honig, B. (1964)
    Theory of Optical and Other Properties of Biopolymers: Applicability and Elimination of the First-Neighbor and Diople-Diople Approximations. Electronic Aspects of Biochemistry.
    Academic Press, New York p77-
  3. Honig, B., Jortner, J. and Szoke, A. (1967)
    Theoretical Studies of Two Photon Absorption: I. Molecular Benzene.
    J. Chem. Phys. 46:2714-2727.
  4. Honig, B. and Jortner, J. (1967)
    Theoretical Studies of Two Photon Absorption: II. Model Calculations.
    J. Chem. Phys. 47:3698-3703.
  5. Scharf, B. and Honig, B. (1970)
    Comments on Vibronic Intensity Borrowing.
    Chem. Phys. Lett. 7:132-136.
  6. Honig, B. and Karplus, M. (1971)
    Implications of Torsional Potential of Retinal Isomers for Visual Excitation.
    Nature 229:558-560.
  7. Honig, B., Hudson, B., Sykes, B. and Karplus, M. (1971)
    Ring Orientation in Beta-ionone and Retinals.
    Proc. Natl. Acad. Sci. USA 68:1289-1293.
  8. Ebrey, T. and Honig, B. (1972)
    Ultraviolet Chromophore Transitions in the Rhodopsin Spectrum.
    Proc. Natl. Acad. Sci. USA 69:1897-1899.
  9. Honig, B., Khan, P., and Ebrey T. (1973)
    Intrinsic Optical Activity of Retinal Isomers: Implications for the Circular Dichroism Spectrum of Rhodopsin.
    Biochem 12:1637-1643.
  10. Honig, B., Kabat, E., Katz, L., Levinthal, C. and Wu, T. (1973)
    Model-Building of Neurohypophyseal Hormones.
    J. Mol. Biol. 80:277-295.
  11. Honig, B. and Ebrey, T. (1974)
    The Structure and Spectra of the Chromophore of the Visual Pigments.
    Ann. Rev. Biophys. Bioeng. 3:151-177.
  12. Chan, W., Nakanishi, K., Ebrey , T. and Honig, B. (1974)
    Properties of 14-Methylretinal, 13-Desmethyl-14-Methylretinal and Visual Pigments Formed Therefrom.
    J. Am. Chem. Soc. 96:3642-3644.
  13. Honig, B., Warshel, A. and Karplus, M. (1975)
    Theoretical Studies of the Visual Chromophore.
    Accounts of Chem. Res. 8:92-100.
  14. Alchalel, A., Honig, B., Ottolenghi, M. and Rosenfeld, T. (1975)
    Triplet Sensitized Cis-Trans Isomerization of Protonated Schiff Bases of Retinal Isomers.
    J. Am. Chem. Soc. 97:2161-2166.
  15. Ebrey, T. and Honig, B. (1975)
    Molecular Aspects of Photoreceptor Function.
    Quart. Rev. Biophys. 8:129-184.
  16. Ebrey, T., Govindjee, R., Honig, B., Pollock, E., Chan , W., Crouch, R., Yudd, A. and Nakanishi, K. (1975)
    Properties of Several Sterically Modified Retinal Analogs and their Photosensitive Pigments.
    Biochem. 14:3933-3941.
  17. Greenberg, A., Honig, B., and Ebrey, T. (1975)
    Wavelength Dependence of Bandwidths of Visual Pigment Spectra.
    Nature 257:823-824.
  18. Honig, B. and Greenberg, A. (1976)
    Chromophore Protein Interactions in Visual Pigments and Their Analogs. Environmental Effects on Molecular Structure and Properties, B. Pullman, Editors,
    D. Reidel Publishing Co., Dordecht-Holland p. 355-362.
  19. Honig, B., Ray, A. and Levinthal, C. (1976)
    Conformational Flexibility and Protein Folding: Rigid structural fragments connected by flexible joints in subtilisin BPN.
    Proc. Natl. Acad. of Sci. 73:1974-1978.
  20. Honig, B., Greenberg, A.D., Dinur, U., and Ebrey, T.G., (1976)
    Visual-Pigment Spectra: Implications of the Protonation of the Retinal Schiff Base.
    Biochem. 15:4593-4599.
  21. Ebrey, T. and Honig, B. (1977)
    New Wavelength Dependent Visual Pigment Nomograms.
    Vision Res. 17:147-151.
  22. Hagler, A. and Honig, B. (1977)
    Theoretical Studies of Protein Folding. In: Peptides Proc. of Fifth American Peptide Symposium. M. Goodman and J. Meienhofer, Editors
    Wiley, New York.
  23. Rosenfeld, T., Honig, B., Ottolenghi, M., Hurley, J. and Ebrey, T. (1977)
    Cis-Trans Isomerization in the Photochemistry of Vision.
    Pure and Appl. Chem 49:341-351.
  24. Callender, R.H. and Honig, B. (1977)
    Resonance Raman Studies of Visual Pigments.
    Ann. Rev. Biophys. Bioeng. 6:33-55.
  25. Stein, W. and Honig, B. (1977)
    Models for Active Transport of Cations--A Steady State Analysis.
    Mol. Cell. Biochem. 15:27-44.
  26. Ebrey T., Becher, B., Mao, B., Kilbride, P. and Honig, B. (1977)
    Exciton Interactions and Chromophore Orientation in the Purple Membrane.
    J. Mol. Biol. 112:377-397.
  27. Hurley, J., Ebrey, T., Honig, B. and Ottolenghi, M. (1977)
    Temperature and Wavelength Effects on the Photochemistry of Rhodopsin, Isorhodopsin, Bacteriorhodopsin and Their Photoproducts.
    Nature 270:540-542.
  28. Yonath, A., Podjarny, A., Honig, B., Sielecki, A. and Traub, W. (1977)
    Crystallographic Studies of Protein Denaturation and Renaturation. 2 Sodium Dodecyl Sulfate Induced Structural Changes in Triclinic Lysozyme.
    Biochem. 16:1418-1424.
  29. Hagler, A. and Honig, B. (1978)
    On the Formation of Protein Tertiary Structure on a Computer.
    Proc. Natl. Acad. Sci. USA 75:554-558.
  30. Honig, B. (1978)
    Light Energy Transduction in Visual Pigments and Bacteriorhodopsin.
    Ann. Rev. Phys. Chem. 29:31-57.
  31. Honig, B. and Stein, W.D. (1978)
    Design Principles for Active Transport Systems.
    J. Theor. Biol. 75:299-305.
  32. Doukas, A.G., Aton, B., Callender, R. and Honig, B. (1978)
    The Resonance Raman Excitation Profile of All-Trans Retinal: Theoretical Implications.
    Chem. Phys. Letts. 56:248-252.
  33. Aton, B., Callender, R. and Honig, B. (1978)
    Photochemical Cis-Trans Isomerization of Bovine Rhodopsin at Liquid Helium Temperatures.
    Nature 273:784-786.
  34. Honig, B. (1978)
    Kinetic and Molecular Models for Proton Pumping in Bacteriorhodopsin. Energetics and Structures of Halophilic Microorganisms, S.R. Caplan and M. Ginzburg, Editors,
    Elsevier/North-Holland Biomedical Press 109-121.
  35. Yonath, A., Podjarny, A., Honig, B., Traub, W., Sielecki, A., Herzberg, O. and Moult, J. (1978)
    Structural Analysis of Denaturant-Protein Interactions: Comparison Between the Effects of Bromoethanol and SDS on Denaturation and Renaturation of Triclinic Lysozyme.
    Biophys. Struct. Mech. 4:27-36.
  36. Nakanishi, K., Balogh-Nair, V., Gawinowicz, M.A., Arnaboldi, M., Motto, M., Honig, B. (1979)
    Double Point Charge Model for Visual Pigments: Evidence From Dihydrorhodopsins.
    Photochem. Photobio. 29:657-660.
  37. Dinur, U. and Honig, B. (1979)
    On the Effects of Methyl Substitution on the Exited States of Butadiene.
    J. Am. Chem. Soc. 101:4453-4460.
  38. Dinur, U. and Honig, B. (1979)
    Natural Orbitals of s-cis-Butadiene and Their Relation to Photochemical Cyclization.
    Chem. Phys. Lett. 64:588-592.
  39. Honig, B., Ebrey, T., Callender, R.H., Dinur, U., and Ottolenghi, M. (1979)
    Photoisomerization, energy storage, and charge separation: A model for light energy transduction in visual pigments and bacteriorhodopsin.
    Proc. Natl. Acad. Sci. USA 76:2503-2507.
  40. Honig, B., Dinur, U., Nakanishi, K., Balogh-Nair, V., Gawinowicz, M.A., Arnaboldi, M, Motto, M. (1979)
    An External Point-Charge Model for Wavelength Regulation in Visual Pigments.
    J. Am. Chem. Soc. 101:7084-7086.
  41. Sheves, M., Nakanishi, K. and Honig, B. (1979)
    Through Space Electrostatic Effects in Electronic Spectra. Experimental Evidence for the External Point Charge Model of Visual Pigments.
    J. Am. Chem. Soc. 101:7086-7088.
  42. Aton, B., Doukas, A., Narva, D., Callender, R., Dinur, U. and Honig, B. (1980)
    Resonance Raman Studies of the Primary Photochemical Event in Visual Pigments.
    Biophys. J. 29:79-94.
  43. Dinur, U. and Honig, B. (1980)
    A Consistent Semiempirical Theory for the Calculation of Ground and Excited State Properties.
    J. Chem. Phys. 72:1817-1829.
  44. Dinur, U., Honig, B. and Schulten, K. (1980)
    On the Nature of Excited Electronic States in Cyanine Dyes: Implications for Visual Pigment Spectra.
    Chem. Phys. Lett. 72:493-497.
  45. Schulten, K., Dinur, U. and Honig, B. (1980)
    The Spectra of Carbonium Ions, Cyanine Dyes, and Protonated Schiff Base Polyenes.
    J. Chem. Phys. 73:3927-3935.
  46. Nakanishi, K., Balogh-Nair, V., Arnaboldi, M., Tsujimoto, K. and Honig, B. (1980)
    An External Point Charge Model for Bacteriorhodopsin to Account for its Purple Color.
    J. Am. Chem. Soc. 102:7945-7947.
  47. Honig, B., Dinur, U., Birge, R., and Ebrey, T.G. (1980)
    The Isomer Dependence of Oscillator Strengths inRetinal and Related Molecules. Spectroscopic Assignments.
    J. Am. Chem. Soc. 102:488-494.
  48. Dinur, U., Honig, B. and Ottolenghi, M. (1981)
    Analysis of Primary Photochemical Processes in Bacteriorhodopsin.
    Photochem. Photobiol. 33:523-527.
  49. Honig, B. (1981)
    Excited State Properties of Visual Pigments and Bacteriorhodopsin.
    Annal. N.Y. Acad. Sci. 376:269-280.
  50. Kalisky, O., Ottolenghi, M., Honig, B. and Korenstein, R. (1981)
    Environmental Effects on the Formation and Photoreaction of the M412 Photoproduct of Bacteriorhodopsin: Implications for the Mechanism of Proton Pumping.
    Biochem 20:649-655.
  51. Doukas, A., Pande, A., Suzuki, T., Callender, R., Honig, B. and Ottolenghi, M. (1981)
    On the Mechanism of Hydrogen-Deuterium Exchange in Bacteriorhodopsin.
    Biophys. J. 33:275-280.
  52. Balogh-Nair, V., Carriker, J.D., Honig, B., Ramat, V., Motto, M.G., Nakanishi, K., Sen, R., Sheves, M., Tanis, M.A. and Tsujimoto, K. (1981)
    The 'Opsin Shift' in Bacteriorhodopsin: Studies with Artificial Bacteriorhodopsins.
    Photochem. Photobiol. 33:483-488.
  53. Honig, B. (1982)
    Photochemical Charge Separation and Active Transport in the Purple Membrane.
    Academic Press, Inc. 16:371-386.
  54. Honig, B. (1982)
    Theoretical Aspects of Photoisomerization in Visual Pigments and Bacteriorhodopsin. Biological Aspects of Ultrafast Laser Spectroscopy, R. Alfano, Editor,
    Academic Press, N.Y. p 281.
  55. Kakitani, T., Honig, B., and Crofts, A.R. (1982)
    Theoretical Studies of the Electrochromic Response of Cartotenoids in Photosynthetic Membranes.
    Biophys. J. 39:57-63.
  56. Eccles, J. and Honig, B. (1983)
    Charged Amino-Acids as Spectroscopic Determinants for Chlorophyll in vivo.
    Proc. Natl. Acad. Sci. USA 80:4959-4962.
  57. Kakitani, T., Kakitani, H., Honig, B. and Nakanishi, K. (1983)
    Symmetric Charge Distribution in Bacteriorhodopsin Binding Site.
    J. Am. Chem. Soc. 105:648-650.
  58. Kakitani, H., Kakitani, T., Rodman, H., Honig, B. and Callender, R. (1983)
    Correlation of Vibrational Frequencies with Absorption Maxima in Polyenes, Rhodopsin, Bacteriorhodopsin and Retinal Analogues.
    J. Phys. Chem. 87:3620-3628.
  59. Honig, B. (1985)
    Electrostatic Interactions in Membrane Proteins.Information and Energy Transduction in Biological Membranes: Proceedings of the International Conference on Biological Membranes, Held in Crans-Sur-Si, L.C. Bolis and E.J. Helmreich, Editors,
    Alan R. Liss, N.Y., N.Y., p 149-152.
  60. Rashin, A. and Honig, B. (1984)
    On the Environment of Ionizable Groups in Globular Proteins.
    J. Mol. Biol. 173:515-521.
  61. Honig, B. and Hubbell, W. (1984)
    Stability of "Salt-bridges"' in Membrane Proteins.
    Proc. Natl. Acad. Sci. USA 81:5412-5416.
  62. Doukas, A.G., Junnarkar, M.R., Alfano, R.R., Callender, R.H., Kakitani, H. and Honig, B. (1984)
    Fluorescene quantum yield of visual pigments: Evidence for Subpicosecond Isomerization Rates.
    Proc. Natl. Acad. Sci. USA 81:4790-4794.
  63. Kakitani, H., Kakitani, T., Rodman, H. and Honig, B. (1985)
    On the Mechanism of Wavelength Regulation in Visual Pigments.
    Photochem. Photobiol. 41:471-479.
  64. Rashin, A.A. and Honig, B. (1985)
    Reevaluation of the Born Model of Ion Hydration.
    J. Phys. Chem. 89:5588-5593.
  65. Gilson, M., Rashin, A., Fine, R. and Honig, B. (1985)
    On the Calculation of Electrostatic Interactions in Proteins.
    J. Mol. Biol. 184:503-516.
  66. Schiffmiller, R., Callender, R., Waddell, W., Govindjee, R., Ebrey, T., Kakitani, H., Honig, B. and Nakanishi, K. (1985)
    Resonance Raman Studies of Bacteriorhodopsin Analogues.
    Photochem. Photobiol. 41:563-567.
  67. Rashin, A. A., Iofin, M. and Honig, B. (1986)
    Internal Cavities and Buried Waters in Globular Proteins.
    Biochem. 25:3619-3623.
  68. Honig, B., Hubbell, W.L. and Flewelling, R.F. (1986)
    Electrostatic Interactions in Membranes and Proteins.
    Ann. Rev. Biophys. Biophys. Chem. 15:163-169.
  69. Gilson, M. and Honig, B. (1986)
    The Dielectric Constant of a Folded Protein.
    Biopolymers 25:2097-2119.
  70. Spudich, J.L., McCain, D.A., Nakanishi, K., Okabe, M., Shimizu, N., Rodman, H., Honig, B. and Bogomolni, R.A. (1986)
    Chromophore/Protein Interaction in Bacterial Sensory Rhodopsin and Bacteriorhodopsin.
    Biophys. J. 49:479-483.
  71. Klapper, I., Hagstrom, R., Fine, R., Sharp, K. and Honig, B. (1986)
    Focusing of Electric Fields in the Active Site of Cu-Zn Superoxide Dismutase: Effects of Ionic Strength and Amino-Acid Modification.
    Proteins: Struc., Func. and Genet. 1:47-59.
  72. Sharp, K., Fine, R., Schulten, K. and Honig, B. (1987)
    Brownian Dynamics Simulations of Diffusion to Irregular Bodies.
    J. Phys. Chem. 91:3624-3631.
  73. Sharp, K., Fine, R. and Honig, B. (1987)
    Computer Simulations of the Diffusion of a Substrate to an Active Site of an Enzyme.
    Sci. 236:1460-1463.
  74. Gilson, M. and Honig, B. (1987)
    Calculation of Electrostatic Potentials in an Enzyme Active Site.
    Nature 330:84-86.
  75. Honig, B. (1987)
    External Point Charges and Amino Sequence in Retinal Proteins. Biophysical Studies of Retinal Proteins. K. Nakanishi, T. Ebrey, B. Honig and H. Frauenfelder, Editors,
    University of Illinois Press, Urbana, IL p.212-218.
  76. Sharp, K., Gilson, M., Fine, R. and Honig, B. (1987)
    Electrostatic Interactions in Proteins.
    Protein Structure, Folding and Design 2, (UCLA Symposia on Mol. Cell. Biol.) Alan R. Liss, Inc. 2:235-244.
  77. Gilson, M., Sharp, K.A. and Honig, B. (1987)
    Calculating the Electrostatic Potential of Molecules in Solution: Method and Error Assessment.
    J. Comp. Chem. 9:327-335.
  78. Gilson, M., Sharp K. and Honig, B. (1988)
    Calculation of the Total Electrostatic Energy of a Macromolecular System: Solvation Energies, Binding Energies, and Conformational Analysis.
    Proteins: Struc., Func. and Genet. 4:7-18.
  79. Gilson, M.K. and Honig, B.H. (1988)
    Energetics of Charge-Charge Interactions in Proteins.
    Proteins: Struc., Func, and Genet. 3:32-52.
  80. Gilson, H., Honig, B., Croteau, A., Zarrilli, G. and Nakanishi, K. (1988)
    Analysis of the Factors Which Influence the C=N Stretching Frequency of Polyene Schiff Bases: Implications for Bacteriorrhodopsin and Rhodopsin.
    Biophys. J. 53:261-269.
  81. Eccles, J., Honig, B. and Schulten, K. (1988)
    Spectroscopic Determinants in the Reaction Center of Rhodopseudomonas viridis.
    Biophys. J. 53:137-144.
  82. Gilson, H. and Honig, B.H. (1988)
    Analysis of NMR and Absorption Spectroscopic Data in Bacteriorhodopsin: Models for Protein Chromophore Interactions.
    J. Am Chem. Soc. 110:1943-1950.
  83. Lanyi, J., Zimanyi, L., Nakanishi, K., Derguini, F., Okabe, M. and Honig, B. (1988)
    Chromophore/Protein and Chromosphore/Anion Interactions in Halorhodopsin.
    Biophys. J. 53:185-191.
  84. Jayaram, B., Fine, R., Sharp, K.A. and Honig, B. (1989)
    Free Energy Calculations of Ion Hydration: An Analysis of the Born Model in Terms of Microscopic Simulations.
    J. Phys. Chem. 93:4320-4327.
  85. Jayaram, B., Sharp, K.A. and Honig, B. (1989)
    The Electrostatic Potential of B-DNA.
    Biopolymers 28:975-993.
  86. Honig, B., Sharp, K. and Gilson, M. (1989)
    Electrostatic Interactions in Proteins. Computer Assisted Modeling of Receptor Ligand Interactions: Theoretical Aspects and Applications to DNA Design, R. Rein and A. Golombek, Editors
    Alan R. Liss, Inc., New York p. 65-74.
  87. Gilson, M. and Honig, B. (1989)
    Destabilization of an alpha-Helix-Bundle by Helix Dipoles.
    Proc. Nat. Acad. Sci. USA 86:1524-1528.
  88. Koutalos, Y., Ebrey, T.G., Tsuda, M., Odashima, K., Lien, T., Park, M.H., Shimizu, N., Derguini, F., Nakanishi, K., Gilson, H. and Honig, B. (1989)
    Regeneration of Bovine and Octopus Opsins in Situ with Natural and Artificial Retinals.
    Biochem. 28:2732-2739.
  89. Chen, J.G., Nakamura, T., Ebrey, T.G., Ok, H., Konno, K., Derguini, F., Nakanishi, K. and Honig, B. (1989)
    Wavelength Regulation in Iodopsin, a Cone Pigment.
    Biophys. J. 55:725-729.
  90. Soman, K., Yang, A.-S., Honig, B. and Fletterick, R. (1989)
    Electrical Potentials in Trypsin Isozymes.
    Biochem. 28:9918-9926.
  91. Sharp, K. and Honig, B. (1989)
    Lattice models of Electrostatic Interaction: The Finite Difference Poisson-Boltzmann Method.
    Chemica Scripta 29A:71.
  92. Sharp, K., Honig, B. and Harvey, S. (1990)
    Electrical Potential of Transfer RNAs: Codon-Anticodon Recognition.
    Biochem. 29:340-346.
  93. Gunner, M. and Honig, B. (1990)
    Electrostatic Analysis of the Midpoints of the Four Hemes in the Bound Cytochrome of the Reaction Center of Rp. Viridis., Perspectives in Photosynthesis. J. Jortner and B. Pullman, Editors
    Kluwer Academic Publishers, Netherlands p. 53-60.
  94. Honig, B. (1990)
    Environmental Effects on Electrostatic Interactions.
    Theoretical Biochemistry & Molecular Biophysics Volume 2: Proteins. David L. Beveridge and Richard Lavery, Editors, Adenine Press 63-67.
  95. Jayaram, B., Swaminathan, S., Beveridge, D., Sharp, K., and Honig, B. (1990)
    Monte Carlo Simulation Studies on the Structure of the Counterion of B-DNA. Variations on the Primitive Dielectric Model.
    Macromolecules 23:3156-3165.
  96. Koutalos, Y., Ebrey, T.G., Gilson, H.R., and Honig, B. (1990)
    Octopus Photoreceptor Membranes. Surface Charge Density and pK of the Schiff Base of the Pigments.
    Biophys. J. 58:493-501.
  97. Sharp, K. and Honig, B. (1990)
    Electrostatic Interactions in Macromolecules: Theory and Applications.
    Ann. Rev. Biophys. Biophys. Chem 19:301-332.
  98. Sharp, K.A. and Honig, B. (1990)
    Calculating Total Electrostatic Energies with the Nonlinear Poisson-Boltzmann Equation.
    J Phys. Chem. 94:7684-7692.
  99. Sharp, K. and Honig, B. (1990)
    Applications of the Finite Defference Poisson-Boltzman Method to Proteins and Nucleic Acids.
    Structure and Methods Vol 2: DNA Protein Complexes & Proteins. Ed. Ramaswamy H. Sarma and Mukti H. Sarma, Adenine Press. p211-214
  100. Gilson, M.K. and Honig, B. (1991)
    The Inclusion of Electrostatic Hydration Energies in Molecular Mechanics Calculations.
    J. Comp. Aided Molecular Design 5:5-20.
  101. Gunner, M.R. and Honig, B. (1991)
    Electrostatic control of midpoint potentials in the cytochrome subunit of the Rhodopseudomonas viridis reaction center.
    Proc. Natl. Acad. Sci. USA. 88:9151-9155.
  102. Honig, B. (1991)
    In Memoriam: Cyrus Levinthal.
    Proteins: Struc., Func. and Genet. 11:239-241.
  103. Jean-Charles, A., Nicholls, A., Sharp, K., Honig, B., Tempczyk, A., Hendrickson, T.F. and Still, W.C. (1991)
    Electrostatic Contributions to Solvation Energies: Comparison of Free Energy Perturbation and Continuum Calculations.
    J. Am. Chem. Soc. 113:1454-1455.
  104. Nicholls, A. and Honig, B. (1991)
    A Rapid Finite Difference Alogrithm, Utililizing Successive Over-Relaxation to Solve the Poisson-Boltzman Equation.
    J. Comp. Chem. 12:435-445.
  105. Sharp, K.A., Nicholls, A., Fine, R., and Honig, B. (1991)
    Reconciling the Magnitude of the Microscopic and Macroscopic Hydrophobic Effects.
    Sci. 252:106-109.
  106. Honig, B. (1991)
    Theory and simulation: Editorial overview.
    Curr. Opinion in Struct. Biol. 1:169-170.
  107. Sharp, K.A., Nicholls, A. , Friedman, R. and Honig, B. (1991)
    Extracting Hydrophobic Free Energies from Experimental Data: Relationship to Protein Folding and Theoretical Models.
    Biochem 30:9686-9697.
  108. Nicholls, A. Sharp, K.A. and Honig, B. (1991)
    Protein Folding and Association: Insights From the Interfacial and Thermodynamic Properties of Hydrocarbons.
    Proteins: Stuc., Func. and Genet. 11:281-296.
  109. Friedman, R.A. and Honig, B. (1992)
    The Electrostatic Contribution to DNA Base- Stacking Interactions.
    Biopolymers 32:145-159.
  110. McGrath, M.E., Vasquez, J.R., Craik, C.S., Yang, A.S., Honig, B., and Fletterick, R.J. (1992)
    Perturbing the Polar Environment of Asp102 in Trypsin: Consequences of Replacing Conserved Ser214.
    Biochem. 31:3059-3064.
  111. Sharp, K., Jean-Charles, A., and Honig, B. (1992)
    A Local Dielectric Constant Model for Solvation Free Energies Which Accounts for Solute Polarizability.
    J. Phys. Chem. 96:3822-3828.
  112. Yang, A.-S. and Honig, B. (1992)
    Electrostatic effects on protein stability.
    Curr. Opinion in Struc. Biol. 2:40-45.
  113. Yang, A.-S, Sharp, K.A. and Honig, B. (1992)
    Analysis of the Heat Capacity Dependence of Protein Folding.
    J. Mol. Biol. 227:889-890.
  114. Gunner, M. and Honig, B. (1993)
    Calculations of Proton Uptake in Rhodobacter Sphaeroides Reaction Centers. The Photosynthetic Bacterial Reaction Centre: Structure, Spectroscopy, and Dynamic,
    J. Breton and Dr. Vermeglio, Editors
    Plenum Publishing Company Ltd., England p.403-410.
  115. Yang, A.-S., Gunner, M.R., Sampogna, R., Sharp, K.A. and Honig, B. (1993)
    On the Calculation of pKas in Proteins.
    Proteins: Struc., Func. and Genet. 15:252-265.
  116. Yang, A.-S. and Honig, B. (1993)
    On the pH Dependence of Protein Stability.
    J. Mol. Biol. 231:459-474.
  117. Honig, B., Sharp, K.A. and Yang, A.-S. (1993)
    Macroscopic Models of Aqueous Solutions: Biological and Chemical Applications.
    J. Phys. Chem. 97:1101-1109.
  118. Gilliam, T.C., Tanzi, R.E., Petrukhin, K., Chernov, I., Pellequer, J.L., Wasco, W., Ross, B., Romano, D.M., Parano, E., Brzustowicz, L.M., Devoto, M., Peppercorn, J., Bush, A.I., Sternieb, I., Pirastu, M., Gusella, J.F., Evgrafov, O., Penchaszadeh, G.K., Honig, B., Edelman, I.S, Soares, M.B., Scheinberg, I.H. (1993)
    The Wilson Disease Gene is a Copper Transporting ATPase with Homology to the Menkes' Disease Gene,
    Nature Genetics 5:344-350.
  119. Smith, K.S. and Honig, B. (1994)
    Evaluation of the Conformational Free Energies of Loops in Proteins.
    Protein 18:119-132.
  120. Monge, A., Freisner, R. and Honig, B. (1994)
    An Algorithm to Generate Low Resolution Protein Tertiary Structures from Secondary Structure Assignments.
    Proc. Natl. Acad. Sci. USA 91:5027-5029.
  121. Misra, V.K., Sharp, K.A. , Friedman, R.A., and Honig, B. (1994)
    Salt Effects on Ligand-DNA Binding. Minor Groove Binding Antibiotics.
    J. Mol. Biol. 238:245-263
  122. Misra, V.A., Hecht, J.L., Sharp, K.A., Friedman, R.A. and Honig, B. (1994)
    Salt Effects on Protein-DNA Interactions. The lambda cI Repressor and EcoRI Endonuclease.
    J. Mol. Biol. 238:264-280.
  123. Sitkoff, D., Sharp, K.A., and Honig, B. (1994)
    Accurate Calculation of Hydration Free Energies Using Macroscopic Solvent Models.
    J. Phys. Chem. 98:1978-1988.
  124. Yang, A. and Honig, B. (1994)
    Structural Origins of pH and Ionic Strength Effects on Protein Stability: Acid Denaturation of Sperm Whale Apomyoglobin.
    J. Mol. Biol. 237:602-614.
  125. Scott, D.L., Mandel, A.M., Sigler, P.B. and Honig, B. (1994)
    The Electrostatic Basis for the Interfacial Binding of Secretory Phospholipases A2.
    Biophys. J. 67:493-504.
  126. Sitkoff, D., Lockhardt., D.J., Sharp, K.A., Honig, B. (1994)
    Calculation of Electrostatic Effects at the Amino Terminus of an alpha-helix.
    Biophys. J. 67:2251-2260.
  127. Sitkoff, D., Sharp, K.A., and Honig, B. (1994)
    Correlating Solvation Free Energies and Surface Tensions of Hydrocarbon Solutes.
    Biophys. Chem. 51:397-409.
  128. Sampogna, R.V. and Honig, B. (1994)
    Environmental Effects on the Protonation States of Active Site Residues in Bacteriorhodopsin.
    Biophys. J. 66:1341-1352.
  129. Tannor, D.J., Marten, B., Murphy, R., Friesner, R.A., Sitkoff, D., Nicholls, A., Ringnalda, M., Goddard III., W.A., Honig, B. (1994)
    Accurate First Principles Calculation of Molecular Charge Distributions and Solvation Energies from Ab Initio Quantum Mechanics and Continuum Dielectic Theory.
    J. Am. Chem. Soc. 116:11875-11882.
  130. Rajasekaran, E., Jayaram, B., and Honig, B., (1994)
    Electrostatic Interactions in Aliphatic Dicarboxylic Acids: A Computational Route to the determination of pKa shifts.
    J. Am. Chem. Soc. 116:8238-8240.
  131. Vorobjev, Y.N., Scheraga, H.A., Hitz, B., Honig, B. (1994)
    Theoretical Modeling of the Electrostatic Effects of Titratable Side-Chain Groups on Protein Conformation in Polar Ionic Solution. I. Potential of Mean Force Between Charged Lysine Residues and Titration of Poly (L-lysine) in 95% Methanol Solution.
    J. Phys. Chem. 98:10940-10948.
  132. Misra, V.K. and Honig, B. (1995)
    On the Magnitude of the Electrostatic Contribution to Ligand-DNA Interactions.
    Proc. Nat. Acad. Sci. USA 92:4691-4695.
  133. Kumar, S.K., Szleiffer., I., Sharp, K.A., Rossky, P., Friedman, R., Honig, B. (1995)
    Size Dependence of Transfer Free Energies A Flory-Huggins Approach.
    J. Phys. Chem. 99:8382-8391.
  134. Honig, B. and Yang, A.-S. (1995)
    Free Energy Balance in Protein Folding.
    Advances in Protein Chemistry 46:27-58.
  135. Bharadwaj, R., Windemuth, A., Sridharan, S., Honig, B., Nicholls, A. (1995)
    The Fast Multipole Boundary Element Method for Molecular Electrostatics: An Optimal Approach for Large Systems.
    J. Comp. Chem. 16:898-913.
  136. Hecht, J.L., Honig, B., Shin, Y.-K., Hubbell, W.L. (1995)
    Electrostatic Potentials Near the Surface of DNA: Comparing Theory and Experiment.
    J. Phys. Chem. 99: 7782-7786.
  137. Sharp,. K.A., Friedman, R.A., Misra, V., Hecht, J., Honig, B. (1995)
    Salt Effects on Polyelectrolyte-Ligand Binding: Comparison of Poisson-Boltzmann, and Limiting/Law Counterion Binding Models.
    Biopolymers 36:245-262.
  138. Vorobjev, Y.N. Scheraga, H.A., Honig, B. (1995)
    Theoretical Modeling of the Electrostatic Effects of Titratable Side-Chain Groups on Protein Conformation in Polar Ionic Solution. pH-Induced Helix-Coil Transition of Poly (l-lysine) in Water and Methanol Ionic Solutions.
    J. Phys. Chem. 99:7180-7187.
  139. Honig, B. and Nicholls, A. (1995)
    Classical Electrostatics in Biology and Chemistry.
    Sci. 268:1144-1149.
  140. Friedman, R.A.and Hong, B. (1995)
    A Free Energy Analysis of Nucleic Acid Base Stacking in Aqueous Solution.
    Biophys. J. 69:1528-1535.
  141. Sharp, K.A. and Honig, B. (1995)
    Salt Effects on Nucleic Acids.
    Curr. Opinion in Struc. Biol. 5:323-328.
  142. Yang, A.-S. and Honig, B. (1995)
    Free Energy Determinants of Secondary Structure Formation: I. alpha-Helices.
    J. Mol. Biol. 252:351-365.
  143. Yang, A.-S. and Honig, B. (1995)
    Free Energy Determinants of Secondary Structure Formation: II. Antiparallel beta-Sheets,
    J. Mol. Biol. 252:366-376.
  144. Honig, B., Ottolenghi, M., and Sheves, M. (1995)
    Acid-Base Equilibria and the Proton Pump in Bacteriorhodopsin.
    Israel J. Chem. 35:429-446.
  145. Sitkoff, D., Ben-Tal, N., and Honig, B. (1996)
    Calculation of Alkane to Water Solvation Free Energies Using Continuum Solvent Models.
    J. Phys. Chem. 100:2744-2752.
  146. Misra, V.K. and Honig, B. (1996)
    The Electrostatic Contribution to the B to Z Transition of DNA.
    Biochem. 35:1115-1123.
  147. Ben-Tal, N., Ben-Shaul, A., Nicholls, A., and Honig, B. (1996)
    Free-Energy Determinants of alpha-Helix Insertion into Lipid Bilayers.
    Biophys. J. 70:1803-1812.
  148. Ben-Shaul, A., Ben-Tal, N., and Honig, B. (1996)
    Statistical Thermodynamic Analysis of Peptide and Protein Insertion into Lipid Membranes.
    Biophys. J. 71:130-137.
  149. Yang, A.-S., Hitz, B., and Honig, B. (1996)
    Free Energy Determinants of Secondary Structure Formation: III. beta-Turns and their Role in Protein Folding
    J. Mol. Bio. 259:873-882.
  150. Sampogna, R.V. and Honig, B. (1996)
    Electrostatic Coupling Between Retinal Isomerization and the Ionization State of Glu-204: A General Mechanism for Proton Release in Bacteriorhodopsin.
    Biophys. J. 71:1165-1171.
  151. Gunner, M.R., Nicholls, A., and Honig, B. (1996)
    Electrostatic Potentials in Rhodopseudomonas viridis Reaction Centers: Implications for the Driving Force and Directionality of Electron Transfer.
    J. Phys. Chem. 100:4277-4291.
  152. Lancaster, C.R.D., Michel, H., Honig, B., and Gunner, M.R. (1996)
    Calculated Coupling of Electron and Proton Transfer in the Photosynthetic Reaction Center of Rhodopseudomonas viridis.
    Biophys. J. 70:2469-2492.
  153. Honig, B. and Cohen, F., (1996)
    Adding Backbone to Protein Folding: Why proteins are polypeptides.
    Folding & Design 1:R17-R20.
  154. Marten, B., Kim, K., Cortis, C., Friesner, R.A., Murphy, R.B., Ringnalda, M.N., Sitkoff, D. and Honig, B., (1996)
    New Model for Calculation of Solvation Free Energies: Correction of Self-Consistent Reaction Field Continuum Dielectric Theory for Short Range Hydrogen-Bonding Effects.
    J. Phys. Chem. 100:11775-11788.
  155. Sharp., K. A., Kumar, S., Rossky, P. J., Friedman, R.A. and Honig, B. (1996)
    Size Dependence of Transfer Free Energies. 2 Hard Sphere Models.
    J. Phys. Chem. 100:14166-14177.
  156. Ben-Tal, N., Honig, B., Peltzsch, R. M., Denisov, G., and McLaughlin, S. (1996)
    Binding of Small Basic Peptides to Membranes Containing Acidic Lipids: Theoretical Models and Experimental Results.
    Biophys. J. 71:561-575.
  157. Friedman, R.A.and Honig, B. (1996)
    Response to S.H. Gellman, T.S. Haque, and L.F. Newcomb.
    Biophys. J. 71:3525-3526.
  158. Ben-Tal, N. and Honig, B. (1996)
    Helix-Helix Interactions in Lipid Bilayers.
    Biophys J. 71:3046-3050.
  159. Ben-Tal, N., Sitkoff, D., Topol, I.A., Yang, A.-S., Burt, S.K., and Honig, B. (1997)
    Free Energy of Amide Hydrogen Bond Formation in Vacuum, in Water, and in Liquid Alkane Solution.
    J. Phys. Chem. B. 101:450-457.
  160. Froloff, N., Windemuth, A., and Honig, B. (1997)
    On the calculation of binding free energies using continuum methods: Application to MHC class I protein-peptide interactions.
    Prot. Sci. 6:1293-1301.
  161. Ben-Tal, N., Honig, B., Miller, C., and McLaughlin, S. (1997)
    Electrostatic Binding of Proteins to Membranes. Theoretical Predictions and Experimental Results with Charybdotoxin and Phospholipid Vesicles.
    Biophys. J. 73:1717-1727.
  162. Chen, S-w W. and Honig, B. (1997)
    Monovalent and Divalent Salt Effects on Electrostatic Free Energies Defined by the Nonlinear Poisson-Boltzmann Equation: Application to DNA Reactions.
    J. Phys. Chem. B. 101:9113-9118.
  163. Murray, D., Ben-Tal, N., Honig, B., and McLauglin, S. (1997)
    Electrostatic Interaction of Myristoylated Proteins with Membranes: Simple Physics, Complicated Biology.
    Structure 5:985-989.
  164. Honig, B. (1997)
    New Challenges in Computational Biochemistry.
    Pacific Symposium on Biocomputing 21:21-24.
  165. Murray, D., Hermida-Matsumoto, L., Buser, C.A., Tsang, J., Sigal, C.T., Ben-Tal, N., Honig, B., Resh, M.D., and McLaughlin, S. (1998)
    Electrostatics and the Membrane Association of Src: Theory and Experiment.
    Biochemistry 37:2145-2159.
  166. Misra, V., Hecht, J., Yang, A.-S., and Honig, B. (1998)
    Electrostatic Contributions to the Binding Free Energy of the lambda cI Repressor to DNA.
    Biophys. J. 75:2262-2273.
  167. Nayal, M., Hitz, B.C., and Honig, B. (1999)
    GRASS: A Server for the Graphical Representation and Analysis of Structures.
    Prot. Sci. 8:676-679.
  168. Xiao, L. and Honig, B. (1999)
    Electrostatic Contributions to the Stability of Hyperthermophilic Proteins.
    J. Mol. Biol. 289:1435-1444.
  169. Nielsen, J. E., Andersen, K. V., Honig, B., Hooft R. W. W., Klebe, G., Vriend, G., and Wade, R. C. (1999)
    Improving macromolecular electrostatics calculations.
    Protein Eng. 12: 657-662.
  170. Yang, A.-S. and Honig, B. (1999)
    Sequence to Structure Alignment in Comparative Modeling using PrISM.
    Proteins: Struc., Func. and Genet. Suppl.3:66-72.
  171. Honig, B. (1999)
    Protein Folding: From the Levinthal Paradox to Structure Prediction.
    J. Mol. Biol. 293:283-293.
  172. Chin, K., Sharp, K., Honig, B. and Pyle, A. M. (1999)
    Calculating the Electrostatic Properties of RNA Provides New Insights Into Molecular Interactions and Function.
    Nat. Struct. Biol. 6:1055-1061.
  173. Polticelli, F., Ascenzi, P., Bolgonesi, M. and Honig, B. (1999)
    Structural Determinants of Trypsin Affinity and Specificity for Cationic Inhibitors.
    Prot. Sci. 8:2621-2629.
  174. Murray, D., Arbuzova, A., Mihaly, G., Gambir, A., Ben-Tal, N., Honig, B. and McLaughlin, S. (1999)
    Electrostatic Properties of Membranes Containing Acidic Lipids and Adsorbed Basic Peptides: Theory and Experiment.
    Biophys. J. 77:3176-3188.
  175. Sheinerman, F., Norel, R. and Honig, B. (2000)
    Electrostatic Aspects of Protein-protein Interactions.
    Curr. Opinion in Struc. Biol. 10:153-159.
  176. Yang, A.-S. and Honig, B. (2000)
    An Integrated Approach to the Analysis of Sequence and Structure. I. Protein Structural Alignment and a Quantitative Measure for Protein Structural Distance.
    J. Mol. Biol. 301: 665-678.
  177. Yang, A.-S. and Honig, B. (2000)
    An Integrated Approach to the Analysis of Sequence and Structure. II. On the Relationship Between Sequence and Structural Similarity for Proteins that are not Obviously Related in Sequence.
    J. Mol. Biol. 301: 679-689.
  178. Yang, A.-S. and Honig, B. (2000)
    An Integrated Approach to the Analysis of Sequence and Structure. III. A Comparative Study of Sequence Conservation in Protein Structural Families Using Multiple Structural Alignments.
    J. Mol. Biol. 301: 691-711.
  179. Arbuzova, A., Wang, L., Wang, J., Hangyás-Mihályné, G., Murray, D., Honig, B. and McLaughlin, S. (2000)
    Membrane Binding of Peptides Containing Both Basic and Aromatic Residues. Experimental Studies with Peptides Corresponding to the Scaffolding Region of Caveolin and the Effector Region of MARCKS.
    Biochemistry 39: 10330-10339.
  180. Ben-Tal, N., Honig, B., Bagdassarian, C. K. and Ben-Shaul, A. (2000)
    Association Entropy in Adsorption Processes.
    Biophys. J. 79:1180-1187.
  181. Petrey, D. and Honig, B. (2000)
    Free Energy Determinants of Tertiary Structure and the Evaluation of Protein Models.
    Protein Science 9:2181-2191.
  182. Al-Lazikani, B., Jung, J., Xiang, Z., and Honig, B. (2001)
    Protein Structure Prediction.
    Curr. Opinion in Chem. Biol. 5:51-56.
  183. Gerstein, M and Honig, B. (2001)
    Sequences and Topology.
    Curr. Opinion in Struc. Biol. 11:327-329.
  184. Norel, R., Sheinerman, F., Petrey, D. and Honig, B. (2001)
    Electrostatics Contributions to Protein-Protein Interactions: Fast Energetic Filters for Docking and Their Physical Basis.
    Prot. Sci. 10:2147-2161.
  185. Xiang, Z. and Honig, B. (2001)
    Extending the Accuracy Limits of Prediction for Side Chain Conformations.
    J. Mol. Biol. 311:421-430.
  186. Rocchia, W., Alexov, E. and Honig, B. (2001)
    Extending the Applicability of the Nonlinear Poisson-Boltzman Equation: Multiple Dielectric Constants and Multivalent Ions.
    J. Phys. Chem. B. 105:6507-6514
  187. Murray, D., McLaughlin, S. and Honig, B. (2001)
    The Role of Electrostatic Interactions in the Regulation of the Membrane Association of G Protein beta-gamma Heterodimers.
    J. Biol. Chem. 276:45153-45159.
  188. Al-Lazikani, B., Sheinerman, F. and Honig, B (2001)
    Combining multiple structure and sequence alignments to improve sequence detection and alignment: Application to the SH2 domains of Janus Kinases.
    PNAS 98:14796-14801.
  189. Murray, D. and Honig, B. (2002)
    Electrostatic control of the membrane targeting of C2 domains.
    Mol. Cell. 9:145-154.
  190. Rocchia, W., Sridharan, S., Nicholls, A., Alexov, E., Chiabrera, A and Honig, B. (2002)
    Rapid Grid-Based Construction of the Molecular Surface and the Use of Induced Surface Charge to Calculate Reaction Field Energies: Applications to the Molecular Systems and Geometric Objects.
    J. Comp. Chem. 23:128-137.
  191. Sheinerman, F. and Honig, B. (2002)
    On the Role of Electrostatic Interactions in the Design of Protein- Protein Interfaces.
    J. Mol. Biol. 318:161-177.
  192. Xiang, Z., Soto, C and Honig, B. (2002)
    Evaluating Conformational Free Energies: The Colony Energy and its Application to the Problem of Loop Prediction.
    Proc. Natl. Acad. Sci. USA 99:7432-7437.
  193. Murray, D., Arbuzova, A., Honig, B. and McLaughlin, S. (2002)
    The Role of Electrostatic and Nonpolar Interactions in the Association of Peripheral Proteins with Membranes.
    Curr. Topics in Membranes 52:277-307.
  194. Jacobson, M. P., Friesner, R. A., Xiang, Z. and Honig, B. (2002)
    On the Role of the Crystal Environment in Determining Protein Side Chain Conformations.
    J. Mol. Biol. 320:597-608.
  195. Rost, B., Honig, B., and Valencia, A. (2002)
    Editorial: Bioinformatics in Structural Genomics.
    Bioinformatics 18:897-898.
  196. Alexov, E. and Honig, B. (2002)
    Structural and Energetic Basis of Molecular Recongnition in Handbook of Cell Signaling. R. Bradshaw and E. A. Dennis, Editors
    Academic Press, San Diego, CA. p.11-13.
  197. Petrey, D., Xiang, X., Tang, C. L., Xie, L., Gimpelev, M., Mitors, T., Soto, C. S., Goldsmith-Fischman, S., Kernytsky, A., Schlessinger, A., Koh, I. Y. Y., Alexov, E. and Honig, B. (2003)
    Using Multiple Structure Alignments, Fast Model Building, and Energetic Analysis in Fold Recognition and Homology Modeling.
    Proteins: Struc., Func. and Genet. 53:430-435
  198. Sosinsky, A., Bonin, K., Mann, R. S. and Honig, B. (2003)
    Target Explorer: an automated tool for the identification of new target genes for a specified set of transcription factors.
    Nucleic Acid Res. 31:3598-3592.
  199. Goldsmith-Fischman, S. and Honig, B. (2003)
    Structural Genomics: Computational Methods for Structural Analysis.
    Prot. Sci. 12:1813-1821
  200. Tao, X., Khayat, R., Christendat, D., Savchenko, A., Xu, X., Goldsmith-Fischman, S., Honig, B., Edwards, A., Arrowsmith, C. and Tong, L. (2003)
    Crystal Structures of MTH1187 and Its Yeast Ortholog YBL001c.
    Proteins: Struc., Func. and Genet. 52:478-480.
  201. Ramelot, T. A., Ni, S., Goldsmith-Fischman, S., Cort, J. R., Honig, B. and Kennedy, M. A. (2003)
    Solution structure of Vibrio cholerae protein VC0424: a variation of the ferredoxin-like fold.
    Protein Sci. 12:1556-1560.
  202. Petrey, D. and Honig, B. (2003)
    GRASP2: Visualization, Surface Properties, and Electrostatics of Macromolecular Structures and Sequences.
    Methods in Enzymology. 374: 492-509
  203. Sheinerman, F. B., Al-Lazikani, B. and Honig, B. (2003)
    Sequence, Structure and Energetic Determinants of Phosphopeptide Selectivity of SH2 Domains.
    J. Mol. Biol. 334:823-841
  204. Tang, C. L., Xie, L., Koh, I. Y. Y., Posy, S., Alexov, E. and Honig, B. (2003)
    On the Role of Structural Information in Remote Homology Detection and Sequence Alignment: New Methods Using Hybrid Sequence Profiles.
    J. Mol. Biol. 334:1043-1062
  205. Patel, S. D., Chen, C. P., Bahna, F., Honig, B. and Shapiro, L. (2003)
    Cadherin-Mediated Cell-Cell Adhesion: Sticking Together as a Family.
    Curr. Op. Struc. Biol. 13:690-698
  206. Aramini, J. M., Huang, Y. J., Cort, J. R., Goldsmith-Fischman, S., Xiao, R., Shih, L.-Y., Ho, C. K., Lui, J., Rost, B., Honig, B., Kennedy, M. A., Acton, T. B. and Montelione, G. T. (2003)
    Solution NMR Structure of the 30S Ribosomal Protein S28E From Pyrococcus horikoshii.
    Prot. Sci. 12:2823-2830
  207. Jacobson, M.P., Pincus D.L., Rapp C.S., Day T.J.F., Honig B., Shaw D.E., and Friesner R.A. (2004)
    A hierarchical approach to all-atom loop prediction.
    Proteins: Struct. Funct. Genet. 55:351-367
  208. Xu, D., Liu, G. Xiao, R., Acton, T., Goldsmith-Fischman, S., Honig, B., Montelione, G. and Szyperski, T. (2004)
    NMR Structure of the Hypothetical Protein AQ-1857 Encoded by the Y157 Gene From Aquifex aeolicus Reveals a Novel Protein Fold.
    Proteins: Struct. Funct. Bioinform 54:794-796
  209. Liu, G., Sukumaran, D. K., Xu, D., Chiang, Y., Acton T, Goldsmith-Fischman, S., Honig, B., Montelione, G. T., and Szyperski, T. (2004)
    NMR structure of the hypothetical protein NMA1147 from Neisseria
    Proteins: Struct. Funct. Bioinform 55:756-758
  210. Goldsmith-Fischman, S., Kuzin, A., Edstrom, W. C., Benach, J., Shastry, R., Xiao, R., Acton, T. B., Honig, B., Montelione, G. T. and Hunt, J. F. (2004)
    The SufE Sulfur-acceptor Protein Contains a Conserved Core Structure that Mediates Interdomain Interactions in a Variety of Redox Protein Complexes.
    JMB 344:549-565
  211. Ramelot, T. A., Cort, J. R., Goldsmith-Fischman, S., Kornhaber, G. J., Xiao, R., Shastry, R., Acton, T. B., Honig, B., Montelione, G. T., and Kennedy, M. A. (2004)
    Solution structure of the iron-sulfur cluster assembly protein U (IscU) with zinc bound at the active site.
    JMB 344:567-583
  212. Fleishman, S. J., Harrington, S., Friesner, R. A., Honig, B. and Ben-Tal, N. (2004)
    An Automatic Method for Predicting Transmembrane Protein Structures Using Cryo-EM and Evolutionary Data.
    Biophys. J. 87:3448-3459
  213. Gimpelev, M., Forrest, L. R. and Honig, B. (2004)
    Helical packing uatterns in Membrane and Soluble Proteins.
    Biophys. J. 87:4075-86
  214. Siggers, T., Silkov, A and Honig, B. (2005)
    Structural Alignment of Protein-DNA Interfaces: Insights inot the Determinants of Binding Specificity.
    JMB 345(5):1027-45
  215. Fan, H., Mark, A. E., Zhu, J. and Honig, B. (2005)
    Comparative Study of Generalized Born Models: Protein Dynamics.
    PNAS 102:6760-6764
  216. Zhu, J., Alexov, E. and Honig, B. (2005)
    Comparative Study of Generalized Born Models: Born Radii and Peptide Folding.
    J. Phys. Chem. 109:3008-3022
  217. Murray, D. and Honig, B. (2005)
    To B or Not to B: PIP2 Answers the Question.
    Dev. Cell 8: 138-9
  218. Shen, Y., Goldsmith-Fischman, S., Atreya, H. S., Acton, T., Ma, L., Xiao, R., Honig, B., Montelione and G. T. Szyperski, T. (2005)
    NMR Structure of the 18 kDa Protein CC1736 From Caulobacter Crescentus Identifies a Member of the "START" Domain Superfamily and Suggests Residues Mediating Substrate Specificity.
    Proteins: Struc., Func. and Bioinform. 58:747-750
  219. Wildonger, J., Sosinksy, A., Honig, B. and Mann, R. S. (2005)
    Lozenge Directly Activates Argos and Klumpfuss to regulate Programmed Cell Death.
    Genes and Dev. 19:1034-1039
  220. Forrest, L. R. and Honig, B. (2005)
    An Assessment of the Accuracy of the Methods for Predicting Hydrogen Positions in Protein Structures.
    Proteins: Struct. Funct. Bioinform. 61:296-309
  221. Chen, C. P., Posy, S., Ben-Shaul, A., Shapiro, L. and Honig, B. (2005)
    Specificity of Cell-Cell Adhesion by Classical Cadherins: Critical Role for Low-Affinity Dimerization Through beta-strand Swapping.
    PNAS 102:8531-8536
  222. Siggers, T., Silkov, A and Honig, B. (2005)
    Bending in the Right Direction.
    Structure 13:1400-1401
  223. Petrey, D. and Honig, B. (2005)
    Protein Structure Prediction: Inroads to Biology.
    Mol. Cell. 20:811-819
  224. Murray, P. S., Li, Z., Wang, J., Tang, C. L., Honig, B. and Murray, D. (2005)
    Retroviral Matrix Domains Share Electrostatic Homology: Models for Membrane Binding Function Throughout the Viral Life Cycle.
    Struct. 13:1521-1531
  225. Powers, R., Mirkovic, N., Goldsmith-Fischman, S., Acton, T.B., Chiang, Y., Huang, Y.J., Ma, L., Rajan, P.K., Cort, J.R., Kennedy, M.A., Liu, J., Rost, B., Honig, B., Murray, D. and Montelione, G. (2005)
    Solution Structure of Archaeglobus fulgidis Peptidly-tRNA Hydrolase (Pth2) Provides Evidence for an Extensive Conserved Family of Pth2 Enzymes in Archea, Bacteria, and Eukaryotes.
    Prot. Sci. 14:2849-2861
  226. Nayal, M. and Honig, B. (2006)
    On the Nature of Cavities on Protein Surfaces: Application to the Identification of Drug Binding Sites.
    Proteins: Struc. Func. Bioinform. 63:892-906
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    Type II Cadherin Ectodomain Structures: Implications for Classical Cadherin Specificity.
    Cell 124:1255-1268
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    Searching for Neuronal Left/Right Asymmetry: Genome Wide Analysis of Nematode Receptor-Type Guanylyl Cyclases.
    Genetics 3:131-149.
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    Structural Refinement of Protein Segments Containing Secondary Structure Elements: Local Sampling, Knowledge-Based Potentials and Clustering.
    Proteins: Struct. Func. Bioinform. 65:463-479.
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    On the Accuracy of Homology Modeling and Alignment Methods Applied to Membrane Proteins.
    Biophys. J. 91:508-517.
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    Protein Structure Comparison: Implications for the Nature of ‘Fold Space’, and Structure and Function Prediction.
    Current Opin Struc Biol 16:393-398.
  232. Kolodny, R. and Honig, B. (2006)
    VISTAL – A New 2D Visualization Tool of Protein 3D Structural Alignments.
    Bioinformatics 22:2166-2167.
  233. Lin, Y.-C., Liu, G., Shen, Y., Bertonati, C., Yee, A., Honig, B., Arrowsmith, C. and Szyperski. T. (2006)
    NMR Structure of Protein PA2021 From Pseudomonas aeruginsoa.
    Proteins: Struct. Func. Bioinform. 65:767-770.
  234. Johnston, Jr., R. J., Copeland, J.W., Fasnacht, M., Etchberger, J.F., Liu, J., Honig, B. and Hobert, O. (2006)
    An Unusual Zn-Finger/FH2 Domain Protein Controls a Left/Right Asymmetric Neuronal Fate Decision in C. elegans.
    Dev. 133:3317-3328.
  235. Tang, C. L., Alexov, E., Pyle, A.M. and Honig, B. (2007)
    Calculation of pKas in RNA: On the Structural Origins and Functional Roles of Protonated Nucleotides.
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    Structure-Based Prediction of C2H2 Zinc-Finger Binding Specificity: Sensitivity to Docking Geometry.
    Nucl. Acid Res. 35:1085-1097.
  237. Bertonati, C., Honig, B. and Alexov, E. (2007)
    Poisson-Boltzmann Calculations of Non-Specific Salt Effects on Protein-Protein Binding Free Energies.
    Biophys. J. 92:1891-1899.
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    Discovering Transcriptional Regulatory Regions in Drosophila by a Non-Alignment Method for Phylogentic Footprinting.
    PNAS 104:6305-6310.
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    Prediction of Side-Chain Conformations on Protein Surfaces.
    Proteins: Struct. Func. Bioinform. 66:814-823.
  240. Singarapu, K.K., Liu, G., Xiao, R., Bertonati, C., Honig, B, Montelione, G. and Szyperski, T. (2007)
    NMR Structure of Protein yjbR From Escherichia coli Reveals ‘Double-wing’ DNA Binding Motif.
    Proteins: Struct. Func. Bioinform. 67:501-504.
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    Local Quality Assessment in Homology Models Using Statistical Potentials and Support Vector Machines.
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    Protein Structure Space is Much More Than the Sum of its Folds.
    Nature Struc. and Mol. Biol.14:458
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    Identification of a Chloride Ion Binding Site in Na+/Cl -Dependent Transporters.
    PNAS 104:12761-12766.
    Commentaries
    (2007). Biochemistry Select. Cell 130, 963, 965-963, 965.
    Chin, G. & Yeston, J. (2007). Editor's Choice. Science 317, 872-3.
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    Functional Specificity of a Hox Protein Mediated by the Recognition of Minor Groove Structure.
    Cell 131:530-54
    Commentary
    (2007). In This Issue. Cell 131, 421, 423-421, 423.
  245. Shapiro, L. and Honig, B. (2007)
    Cell - to - Cell Contact and Extracellular Matrix.
    Curr. Opin. Cell Biol. 19: 493-494
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    Loop Modeling: Sampling, Filtering and Scoring.
    Proteins. 70:834-843.
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    Crystal Structure of the Extracellular Cholinsterase-Like Domain from Neuroligin-2.
    Proteins. 105:1873-1878.
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    Crystal Structures of β-Neurexin 1 and β-Neurexin 2 Ectodomains and Dynamics of Splice Insertion Sequence 4.
    Structure 16:410-421.
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    Refining Homology Models by Combining Replica-Exchange Molecular Dynamics and Statistical Potentials.
    Proteins: Struct. Func. Bioinform. 72:1171-1188
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    Sequence and structure determinants of strand swapping in cadherin domains: Do all cadherins bind through the same adhesive interface?
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  251. Forrest, L.R., Zhang, Y.-W., Jacobs, M.T., Gesmonde, J., Xie, L., Honig, B. and Rudnick, G. (2008)
    A Mechanism for Alternating Access in Neurotransmitter Transporters.
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    Kanner, B. I. (2008). Structural biology: It's not all in the family. Nature 454, 593-594.
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  252. Miloushev, V., Bahna, F., Ciatto, C., Ahlsen, G., Honig, B., Shapiro, L. and Palmer, A.G. (2008)
    Dynamic Properties of a Type II Cadherin Adhesive Domain: Implications for the Mechanism of Strand-Swapping of Classical Cadherins.
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    Electrostatic and Lipid-Anchor Contributions to the Interaction of Transducin with Membranes.
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    Is Protein Classification Necessary? Towards Alternate Approaches to Funtion Annotation.
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  255. Schwede, T., Sali, A., Honig, B., Levitt, M., Berman, H.M., Jones, D., Brenner, S.E., Burley, S.K., Das, R., Dokholyan, N.V., Dunbrack Jr., R.L., Fidelis, K., Fiser, A., Godzik, A., Huang, Y.J., Humblet, C., Jacobson, M.P., Joachimiak, A., Krystek Jr., S.R., Kortemme, T., Kryshtafovych, A., Montelione, G.T., Moult, J., Murray, D., Sanchez, R., Sosnick, T.R., Standley, D.M., Stouch, T., Vajda, S., Vasquez, M., Westbrook, J.D. and Wilson, I.A. (2008)
    Outcome of a Workshop on Applications of Protein Models in Biomedical Research.
    Structure 17:151-159.
  256. Rohs, R., West, S.M., Liu, P. and Honig, B. (2009)
    Nuance in the Double-Helix and its Role in Protein-DNA Recognition.
    Curr. Opin. Struc. Biol. 19:171-177.
  257. Katsamba, P., Carroll, K., Ahlsen, G., Bahna, F., Vendome, J., Posy, S., Rajebhosale, M., Price, S., Jessell, T.M., Ben-Shaul, A., Shapiro, L. and Honig, B. (2009)
    Linking Molecular Affinity and Cellular Specificity in Cadherin-Mediated Adhesion.
    Proc. Natl. Acad. of Sci. 106:11594-11599.
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    Structural Relationships Among Proteins With Different Global Topologies and Their Implications for Function Annotation Strategies.
    Proc. Natl. Acad. of Sci. 106:17377-17382.
  259. Rossi, P., Aramini, J.M., Xiao, R., Chen, C.X., Nwosu, C., Owens, L.A., Maglaqui, M., Nair, R., Fischer, M., Acton, T.B., Honig, B., Rost, B., and Montelione, G.T. (2009)
    Structural Elucidation of the Cys-His-Glu-Asn Proteolytic Relay in the Secreted CHAP Domain Enzyme From the Human Pathogen Staphylococcus saprophyticus.
    Proteins: Struct. Func. Bioinform. 74:515-519.
  260. Rohs, R., West, S.M., Sosinsky, A., Liu, P., Mann, R.S. and Honig, B. (2009)
    The Role of DNA Shape in Protein-DNA Recognition.
    Nature 461:1248-1253
    Commentaries
    Tullius, T. (2009). Structural biology: DNA binding shapes up. Nature 461, 1225-1226.
    HHMI Research News. Studies begin to shape new image of DNA. Research News October 29, 2009
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  261. West, S.M., Rohs, R., Mann, R.S. and Honig B. (2010)
    Electrostatic Interactions Between Arginines and the Minor Groove in the Nucleosome.
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  262. Zhu, J., Cheng, L., Fang, Q., Zhou, H. and Honig, B. (2010)
    Building and Refining Protein Models within Cryo-electron Microscopy Density Maps Based on Homology Modeling and Multiscale Structure Refinement.
    J. Mol. Biol. 397:835-851.
  263. Cheng, L., Zhu, J., Hui, W.H., Zhang, X., Honig, B., Fang, Q. and Zhou, Z.H. (2010)
    Backbone Model of an Aquareovirus Virion by Cryo-Electron Microscopy and Bioinformatics.
    J. Mol. Biol. 397:852-863.
  264. Ciatto, C., Bahna, F., Zampieri, N., Vansteenhouse, H.C., Katsamba, P.S., Ahlsen, G., Harrison, O.J., Brasch, J., Jin, X., Posy, S., Vendome, J., Ranscht, B., Jessell, T.M., Honig, B. and Shapiro, L. (2010)
    T-cadherin Structures Reveal a Novel Adhesive Binding Mechanism.
    Nat. Struc. Mol. Biol. 17:339-347.
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    Two-Step Adhesive Binding by Classical Cadherins.
    Nat. Struc. Mol. Biol. 17:348-358.
  266. Singarapu, K.K., Mills, J.L., Xiao, R., Acton, T., Punta, M., Fisher, M., Honig, B., Rost, B., Montelione, G.T., Szyperski, T. (2010)
    Solution NMR Structures of Proteins VPA0419 from Vibrio parahaemolyticus and yiiS form Shigella flexneri Provide Structural Coverage for Protein Domain Family PFAM 04175.
    Proteins: Struct. Func. Bioinform. 78:779-784.
  267. Rohs, R., Jin, X., West, S.M., Joshi, R., Honig, B. and Mann, R.S. (2010)
    Origins of Specificity in Protein-DNA Recognition.
    Ann. Rev. Biochem. 79:233-269.
  268. Kitayner, M., Rozenberg, H., Rohs, R., Suad, O., Rabinovich, D., Honig, B. and Shakked, Z. (2010)
    Diversity in DNA Recognition by P53 Revealed by Crystal Structures with Hoogsteen Base Pairs.
    Nat. Struc. Mol. Biol. 17:423-429.
    Commentary
    Chitayata, S. and Arrowsmith, C.H. (2010). Four p(53)s in a Pod. Nat. Struc. Mol. Biol. 17:390-391.
  269. Lee, H., Li, Z., Silkov, A., Fischer, M., Petrey, D., Honig, B., and Murray, D. (2010)
    High-Throughput Computational Structure-Based Characterization of Protein Families: START Domains and Implications for Structural Genomics.
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    Protein Interface Conservation Across Structure Space.
    Proc. Natl. Acad. of Sci. 107:10896-10901.
  271. Norel, R., Petrey, D. and Honig, B. (2010)
    PUDGE: A Flexible, Interactive Server for Protein Structure Prediction.
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    Splice Form Dependence of β-Neurexin/Neuroligin Binding Interactions.
    Neuron 67:61-74.
    Commentary
    Wei, Z. and Zhang, M. (2010). A Structural Approach to Decipher the Neurexin and Neuroligin Splice Isoform Code.Neuron 67:1-2.
  273. Wu, Y., Jin, X., Harrison, O., Shapiro, L., Honig, B. and Ben-Shaul, A. (2010)
    Cooperativity Between trans and cis Interactions in Cadherin-Mediated Junction Formation.
    Proc. Natl. Acad. of Sci. 107:17592-17597.
  274. Chen, B.Y. and Honig, B. (2010)
    VASP: A Volumetric Analysis of Surface Properties Yields Insights into Protein-Ligand Binding Specificity.
    PLoS Comput. Biol. 6:e1000881.
  275. Love, J., Mancia, F., Shapiro, L, Punta, M., Rost, B., Girvin, M., Wang, D.N., Zhou, M., Hunt, J.F., Szperski, T., Gouaux, E., MacKinnon, R., McDermott, A., Honig, B., Inouye, M., Montelione, G. and Hendrickson, W.A. (2010)
    The New York Constorium on Membrane Protein Sturcture (NYCOMPS): A High-Throughput Platform for Structural Genomics of Integral Membrane Proteins.
    J. Struc. Func. Genomics 11:191-199.
  276. Behnke-Parks, W.M., Vendome, J., Honig, B., Maliga, Z., Moores, C. and Rosenfeld, S.S. (2011)
    Loop L5 Acts As a Conformational Latch in the Mitotic Kinesin eg5.
    J. Biol. Chem. 286:5242-5253.
  277. Brasch, J., Harrison, O.J., Ahlsen, G., Carnally, S.M., Henderson, R.M., Honig, B. and Shapiro, L. (2011)
    Structure and Binding Mechanism of Vascular Endothelial Cadherin: A Divergent Classical Cadherin.
    J. Mol. Biol. 408:57-73.
  278. Harrison, O.J., Jin, X., Hong, S., Bahna, F., Ahlsen, G., Brasch, J., Wu, Y., Vendome, J., Felsovalyi, K., Hampton, C.M., Troyanovsky, R.B., Ben-Shaul, A., Troyanovsky, S.M., Shapiro, L. and Honig, B. (2011)
    The Extracellular Architecture of Adherens Junctions Revealed By Crystal Structures of Type I Cadherins.
    Structure 19:244-256.
  279. Honig, B. and Rohs, R. (2011)
    Biophyics: Flipping Watson and Crick.
    Nature 470:472-473.
  280. Fischer, M., Honig, B. and Petrey, D. (2011)
    MarkUs: A Server to Navigate Sequence-Structure-Function Space.
    Nucl. Acid Res. 39:W357-W361.
  281. Vendome, J., Posy, S., Jin, X., Bahna, F., Ahlsen, G., Shapiro, L. and Honig, B. (2011)
    Molecular Design Principles Underlying β-strand Strand Swapping in the Adhesive Dimerization of Classical Cadherins.
    Nat. Struc. Mol. Biol. 18:693-700.
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    Transforming Binding Affinities from Three Dimension to Two With Application to Cadherin Clustering.
    Nature 475:510-513.
  283. Zhang, Q.Z., Deng, L., Fischer, M., Guan, J., Honig, B. and Petrey, D. (2011)
    PredUs: A Web Server for Predicting Protein Interfaces Using Structural Neighbors.
    Nucl. Acid Res. 39:W283-W287.
  284. Zhu, J., Yu, Y., Ulbrich, M.H., Li, M.-H., Isacoff, E.Y., Honig, B.H. and Yang, J. (2011)
    Structural Model of the TRPP2/PKD1 C-terminal Coiled-coil Complex Produced by a Combined Computational and Experimental Approach.
    Proc. Natl. Acad. of Sci. 108:10133-10138.
  285. Kuziemko, A., Honig, B. and Petrey, D. (2011)
    Using Structure to Explore the Sequence Alignment Space of Remote Homologs.
    PLoS Comput. Biol. 10:e1002175.
  286. Bishop, E.P., Rohs,R., Parker, S.C., West, S.M., Liu, P., Mann, R.S., Honig, B. and Tullius, T.D. (2011)
    A Map of Minor Groove Shape and Electrostatic Potential From Hydroxyl Radical Cleavage Patterns of DNA.
    ACS Chem Biol 6:1314-1320.
  287. Slattery, M., Riley, T., Liu, P., Abe, N., Gomez-Alcala, P., Dror, I., Zhou, T., Rohs, R., Honig, B., Bussemaker, H.J. and Mann, R.S. (2011)
    Cofactor Binding Evokes Latent Differences in DNA Binding Specificity Between Hox Proteins.
    Cell. 147:1270-1282.
    Commentary
    Ansari, A.Z. and Peterson-Kaufman, K.J. (2011). A Partner Evokes Latent Differences Between Hox Proteins. Cell 147:1220-1221.
  288. Jin, X., Walker, M.A., Felsovalyi, K., Vendome, J., Bahna, F., Mannepalli, S., Cosmanescu, F., Ahlsen, G., Honig, B. and Shapiro, L. (2012)
    Crystal Structures of Drosophila N-cadherin Ectodomain Regions Reveal a Widely Used Class of Ca2+-free Interdomain Linkers.
    Proc. Natl. Acad. of Sci. 108:10133-10138.
  289. Floratos, A., Honig, B., Pe’er, D. and Califano, A. (2012)
    Using Systems and Structure Biology Tools to Dissect Cellular Phenotypes.
    J. Amer. Med. Inform. Assoc. 19:171-175
  290. Eletsky, A., Petrey, D., Zhang, Q.C., Lee, H.W., Acton, T.B., Xiao, R., Everett, J.K., Prestegard, J.H., Honig, B., Montelione, G.T. and Szyperski, T. (2012)
    Solution NMR Structures Reveal Unique Homodimer Formation by a Winged Helix-Turn-Helix Motif and Provide First Structures for Protein Domain Family PF10771.
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  291. Chen, Y., Sheng, R., Kallberg, M., Silkov, A., Tun, M.P., Bhardwaj, N., Kurilova, S., Hall, R.A., Honig, B., Lu, H. and Cho, W. (2012)
    Genome-Wide Identification and Functional Annotation of Dual Specificity Protein- and Lipid-Binding Modules that Moderate Protein Interactions at the Membrane.
    Mol. Cell 46:226-237
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    Thinking Outside the Cell: How Cadherins Drive Adhesion.
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  293. Zhang, Q.C., Petrey, D., Deng, L., Qiang, L., Shi Y., Thu, C.A., Bisikirska B., Lefebvre C., Accili D., Hunter, T., Maniatis, T., Califano, A. and Honig, B. (2012)
    Structure-based prediction of protein-protein interactions on a genome-wide scale.
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    Nectin Ectodomain Structures Reveal a Canonical Adhesive Interface.
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    PrePPI: a structure-informed database of protein-protein interactions.
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    Towards a “Structural BLAST”: Using Structural Relationships to Infer Function.
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    Theory and Simulations of Adhesion Receptor Dimerization on Membrane Surfaces.
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    Mechanism of E-Cadherin Dimerization Probed by NMR Relaxation Dispersion.
    Proc. Natl. Acad. of Sci. 110: 16462-16467.
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    OnTheFly: A Database of Drosophila melanogaster Transcription Factors and Their Binding Sites.
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    Structural Bioinformatics of the Interactome.
    Ann. Rev. Biophysics In Press.
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