1985 1986 1987 1988 1989 1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 Books

Back to Top

Publications in Refereed Journals

    1985

  1. MacKerell, Jr. A.D. Vallari, R.C. and Pietruszko, R. "Human mitochondrial aldehyde dehydrogenase inhibition by diethyldithiocarbamic acid methanethiol mixed disulphide: A derivative of disulfiram," FEBS Letters 179:77-81, 1985.
  2. 1986

  3. MacKerell, Jr. A.D. Blatter, E.E. and Pietruszko, R. "Human aldehyde dehydrogenase: Kinetic identification of the isozymes for which biogenic aldehydes and acetaldehyde compete," Alcoholism: Clinical and Experimental Research 10: 266-277, 1986.
  4. MacKerell, Jr. A.D. McWright, R.S. and Pietruszko, R. "Bromoacetophenone as an affinity reagent for human aldehyde dehydrogenase," Biochemistry 25: 5182-5189, 1986.
  5. MacKerell, Jr. A.D. and Pietruszko, R. "Chemical modification of human aldehyde dehydrogenase by substrate," Biophysica Biochemica Acta 911: 306-317, 1986.
  6. 1987

  7. MacKerell, Jr. A.D. Rigler, R. Nilsson, L. Hahn, U. and Saenger, W. "Protein Dynamics: A time-resolved fluorescence, energetic and molecular dynamics study of ribonuclease T1," Biophysical Chemistry 26: 247-261, 1987.
  8. Abriola, D.P. Fields, R. Stein, S. MacKerell, Jr. A.D. and Pietruszko, R. "Active-site identification of human aldehyde dehydrogenase," Biochemistry 26: 5679-5684, 1987.
  9. 1988

  10. MacKerell, Jr. A.D. Nilsson, L. Rigler, R. and Saenger, W. "Molecular dynamic simulations of ribonuclease T1: Analysis of the effect of solvent on the structure, fluctuations and active site of the free enzyme," Biochemistry 27: 4547-4556, 1988.
  11. MacKerell, Jr. A.D. "Molecular modeling and dynamics of neuropeptide Y," Journal of Computer-Aided Molecular Design 2: 55-63, 1988.
  12. MacKerell, Jr. A.D. Rigler, R. Nilsson, L. Heinemann, U. and Saenger, W. "Molecular dynamic simulations of ribonuclease T1: Effect of solvent on the interaction with 2'GMP," European Biophysics Journal 16: 287-297, 1988.
  13. 1989

  14. MacKerell, Jr. A.D. Hemsen, A. Lacroix, J.S. and Lundberg, J.M. "Analysis of structure-function relationships of neuropeptide Y using molecular dynamics simulations and pharmacological activity measurements," Regulatory Peptides 25: 295-313, 1989.
  15. MacKerell, Jr. A.D. Nilsson, L. Rigler, R. Heinemann, U. and Saenger, W. "Molecular dynamic simulations of ribonuclease T1: Comparison of the free enzyme and the 2'GMP-enzyme complex," Proteins: Structure, Function and Genetics 6: 20-31, 1989.
  16. Chen, E. Soderberg, P.G. MacKerell, Jr. A.D. Lindstrom, B. and Tengroth, B.M. "Inactivation of lactate dehydrogenase by UV radiation in the 300 nm wavelength region," Radiation and Environmental Biophysics 28: 185-191, 1989.
  17. 1990

  18. Abriola, D.P. MacKerell, Jr. A.D. and Pietruszko, R. "Human aldehyde dehydrogenase: Correlation of activity loss with 14C-bromoacetophenone into glutamate 268 and cysteine 302; Quarter-of-the-sites reactivity of aldehyde dehydrogenase," Biochemical Journal 266: 179-187, 1990.
  19. 1991

  20. MacKerell, Jr. A.D. Rigler, R. Hahn, U. and Saenger, W. "Thermodynamic analysis of the equilibrium, association, and dissociation of 2'GMP and 3'GMP with Ribonuclease T1 at pH 5.3," Biochimica et Biophysica Acta 1073: 357-365, 1991.
  21. MacKerell, Jr. A.D. "Principles and methods in molecular modeling and dynamics of biologically active peptides: Application to neuropeptide Y," Methods in Enzymology 202: 449-470, 1991.
  22. MacKerell, Jr. A.D. and Karplus, M. "Importance of attractive van der Waals contribution in empirical energy function models for the heat of vaporization of polar liquids," Journal of Physical Chemistry 95: 10559-10560, 1991.
  23. 1993

  24. Uvdal, P. MacKerell, Jr. A.D. and Wiegand, B.C. "Intramolecular vibrational coupling of adsorbates probed using HREELS and ab initio calculations: ethoxides absorbed on Mo(110)," Journal of Electron Spectroscopy and Related Phenomena 64/65: 193-199, 1993.
  25. 1994

  26. Yang, B. Wright, J. Eldefrawi, M.E. Poi, S.and MacKerell, Jr. A.D. "Conformational, aqueous solvation and pKa contributions to the binding of cocaine, WIN and a WIN vinyl analog," Journal of the American Chemical Society 116: 8722-8732, 1994.
  27. 1995

  28. MacKerell, Jr. A.D. "Molecular dynamics simulation analysis of a sodium dodecyl sulfate micelle in aqueous solution: Decreased fluiditiy of the micelle hydrophobic interior," Journal of Physical Chemistry 99: 1846-1855, 1995.
  29. MacKerell, Jr. A.D. Sommer, M.S. and Karplus, M. "pH Dependence of binding reactions from free energy simulations and macroscopic continuum electrostatic calculations: Application to 2'GMP/3'GMP binding to ribonuclease T1," Journal of Molecular Biology 247: 774-807, 1995.
  30. Uvdal, P. MacKerell, Jr. A.D. Wiegand, B.C. and Friend, C.M. "Surface-induced alteration of adsorbate intramolecular vibrational coupling: 2-propoxide on Mo(110) as determined by ab initio calculations and experiments," Physical Review B 51: 7844-7848, 1995.
  31. MacKerell, Jr. A.D. Wiorkiewicz, J.K. and Karplus, M. "All-atom empirical energy function for the simulation of nucleic acids," Journal of the American Chemical Society 117: 11946-11975, 1995.
  32. 1996

  33. Yin, D. and MacKerell, Jr. A.D. "Ab initio calculations on the use of Helium and Neon as probes of van der Waals surfaces of molecules," Journal of Physical Chemistry 100: 2588-2596, 1996.
  34. Ho, L.L. MacKerell, Jr. A.D. and Bash, P.A. "Proton and Hydride Transfers in Solution (I): Hybrid, QM/MM Free Energy Perturbation Study," Journal of Physical Chemistry 100: 4466-4475, 1996.
  35. Bash, P.A. Ho, L.L. MacKerell, Jr. A.D. Levine, D. and Hallstrom, P. "Progress toward Chemical Accuracy in the Computer Simulations of Condensed Phase Reactions," Proceedings of the National Academy of Sciences, USA 93: 3698-3703, 1996.
  36. Feng, M.-H. Philippopoulos, M. MacKerell, Jr. A.D. and Lim, C. "Structural Characterization of the Phosphotyrosine Binding Region of a High-Affinity SH2 Domain-Phosphopeptide Complex by Molecular Dynamics Simulation and Chemical Shift Calculations," Journal of the American Chemical Society 118: 11265-11277, 1996.
  37. 1997

  38. Pavelites, J.J. Bash, P.A. Gao, J. and MacKerell, Jr. A.D. "A Molecular Mechanics Force Field for NAD+, NADH and the Pyrophosphate Groups of Nucleotides," Journal of Computational Chemistry, 18: 221-239, 1997.
  39. Li, Y. MacKerell, Jr. A.D. Egorin, M.J. Ballesteros, M.F. Rosen, D.M. Wu, Y.-Y. Blamble, D.A. and Callery, P.S. "Structure-Function Relationships of Polyamine Transport Inhibitors in L1210 Murine Leukemia Cells," Cancer Investigation 57: 234-239, 1997.
  40. MacKerell, Jr. A.D. "Influence of Magnesium Ions on Duplex DNA Structural, Dynamic and Solvation Properties," Journal of Physical Chemistry B 101: 646-650, 1997.
  41. Feller. S.E. Yin, D. Pastor, R.W. and MacKerell, Jr. A.D. "Molecular Dynamics Simulation of Unsaturated Lipids at Low Hydration: Parametrization and Comparison with Diffraction Studies," Biophysical Journal 73: 2269-2279, 1997.
  42. MacKerell, Jr. A.D. "Influence of Water and Sodium on the Energetics of Dimethylphosphate and its Implications For DNA Structure," Journal de Chimie Physique 94:1436-1447, 1997.
  43. Uvdal, P. and MacKerell, Jr. A.D. "Vibrational Spectrum of Methoxy Adsorbed on Metal Surfaces: Ab initio Calculations and Experiments," Surface Science 393: 141-149, 1997.
  44. 1998

  45. Yin, D. and MacKerell, Jr. A.D. "Combined Ab initio/Empirical Approach for the Optimization of Lennard-Jones Parameters," Journal of Computational Chemistry 19: 334-338, 1998.
  46. Lieske, S. Yang, B. Eldefrawi, M.E. and MacKerell, Jr. A.D. and Wright, J. "(-)3-Substituted Ecgonine Methyl Esters as Inhibitors for Cocaine Binding and Dopamine Uptake," Journal of Medicinal Chemistry 41: 864-876, 1998.
  47. MacKerell, Jr. A.D. Bashford, D. Bellott, M. Dunbrack Jr. R.L. Evanseck, J. Field, M.J. Fischer, S. Gao, J. Guo, H. Ha, S. Joseph, D. Kuchnir, L. Kuczera, K. Lau, F.T.K. Mattos, C. Michnick, S. Ngo, T. Nguyen, D.T. Prodhom, B. Reiher, III, W. E. Roux, B. Schlenkrich, M. Smith, J. Stote, R. Straub, J. Watanabe, M. Wiorkiewicz-Kuczera, J. Yin, D. and Karplus, M. "All-atom empirical potential for molecular modeling and dynamics studies of protein," Journal of Physical Chemistry B 102: 3586-3616, 1998.
  48. Foloppe, N. and MacKerell, Jr. A.D. "Conformational Properties of the Deoxyribose and Ribose Moieties of Nucleic Acids: A Quantum Mechanical Study," Journal of Physical Chemistry B 102: 6669-6678, 1998.
  49. 1999

  50. Uvdal, P. Åsmundsson, R. and MacKerell, Jr. A.D. "Experimental vibrational shifts induced by 13C isotopic substitution assigned by ab initio calculations," Physical Review Letters 82: 125-128, 1999.
  51. Pastor, N. MacKerell, Jr. A.D. and Weinstein, H. "TIT for TAT: The Properties of Inosine and Adenosine in TATA Box DNA," Journal of Biomolecular Structure & Design 16: 787-810, 1999.
  52. Lee, G.U. and MacKerell, Jr. A.D. "Force, Energy and Structure of Double-stranded DNA Oligonucleotides under Tensile Load," European Journal of Biophysics 28: 415-426, 1999.
  53. Foloppe, N. and MacKerell, Jr. A.D. "Intrinsic Conformational Properties of Deoxyribosnucleosides: Implicated role for cytosine in the equilibrium between the A, B and Z forms of DNA," Biophysical Journal 76: 3206-3218, 1999.
  54. Foloppe, N. and MacKerell, Jr. A.D. "Contribution of the Phosphodiester Backbone and Glycosyl Linkage Intrinsic Torsional Energetics to DNA Structure and Dynamics," Journal of Physical Chemistry B 103: 10955-10964, 1999.
  55. 2000

  56. Chen, I.-J. and MacKerell, Jr. A.D. "Computation of the influence of chemical substitution on the pKa of pyridine using semiempirical and ab initio methods," Theoretical Chemistry Accounts 103: 483-494, 2000.
  57. Foloppe, N. and MacKerell, Jr. A.D. "All-atom empirical force field for nucleic acids: 1) Parameter optimization based on small molecule and condensed phase macromolecular target data," Journal of Computational Chemistry 21: 86-104, 2000.
  58. MacKerell, Jr. A.D. and Banavali, N. "All-atom empirical force field for nucleic acids: 2) Application to molecular dynamics simulations of DNA and RNA in solution," Journal of Computational Chemistry 21: 105-120, 2000.
  59. Chen, I.J. Neamati, N. Nicklaus, M.C. Orr, A. Anderson, L. Barchi, Jr. J.J. Kelley, J.A. Pommier, Y. and MacKerell, Jr. A.D. "Identification of HIV-1 Integrase Inhibitors via Three-Dimensional Database Searching using ASV and HIV-1 Integrases as Targets," Bioroganic & Medicinal Chemistry 8: 2385-2389, 2000.
  60. Barsky, D. Foloppe, N. Ahmadia, S. Wilson, III, D.M. and MacKerell, Jr. A.D. "New Insights into the Structure of Abasic DNA from Molecular Dynamics Simulations," Nucleic Acids Research 28: 2613-2626, 2000.
  61. Feller, S.E. and MacKerell, Jr. A.D. "An Improved Empirical Potential Energy Function for Molecular Simulations of Phospholipids," Journal of Physical Chemistry B 104: 7510-7515, 2000.
  62. Ásmundssson, R. Uvdal, P. and MacKerell, Jr. A.D. "Binary combination and overtone modes in the C-H stretch region in ethoxy adsorbed on Cu(100): Experimental and calculated vibrational spectra," Journal of Chemical Physics 113: 1258-1267, 2000.
  63. Wang, P. Nicklaus, M.C. Marquez, V.E. Brank, A.S. Christman, J. Banavali, N.K. and MacKerell, Jr. A.D. "Use of Oligodeoxyribonucleotides with Conformationally Constrained Abasic Sugar Targets to Probe the Mechanism of Base Flipping by HhaI DNA (Cytosine C5)-Methyltransferase," Journal of the American Chemical Society 122: 12422-12434, 2000.
  64. 2001

  65. Banavali, N.B. and MacKerell, Jr. A.D. "Reevaluation of Stereoelectronic Contributions to the Conformational Properties of the Phosphodiester and N3'-Phosphoramidate Moieties of Nucleic Acids," Journal of the American Chemical Society 123: 6747-6755, 2001.
  66. Marquez, V.E. Wang, P. Nicklaus, M.C. Maier, M. Manoharan, M. Christman, J.K. Banavali, N.K. and MacKerell, Jr. A.D. "Inihibition of (Cytosine C5)-Methyltransferase by Oligonucleotides Containing Flexible (Cyclopentane) and Conformationally Constrained (Bicyclo[3.1.0]hexane) abasic sites," Nucleosides, Nucleotides and Nucleic Acids 20:451-450, 2001.
  67. MacKerell, Jr. A.D. Banavali, N.B. and Foloppe, N. "Development and Current Status of the CHARMM Force Field for Nucleic Acids," Biopolymers 56: 257-265, 2001.
  68. Izaguirre, G. Pietruszko, R. Cho, S. and MacKerell, Jr. A.D. "Human Aldehyde Dehydrogenase Catalytic Activity and Structural Interactions with Coenzyme Analogs," Journal of Biomolecular Structure and Dynamics 19: 429-448, 2001.
  69. Banavali, N.B. and MacKerell, Jr. A.D. "Reexamination of the Intrinsic, Dynamic, and Hydration Properties of Phosphoramidate DNA," Nucleic Acids Research 29: 3219-3230, 2001.
  70. 2002

  71. Chen, I.-J. Yin, D. and MacKerell, Jr. A.D. "Combined Ab initio/Empirical Approach for Optimization of Lennard-Jones Parameters for Polar-Neutral Compounds," Journal of Computational Chemistry, 23: 199-213, 2002.
  72. Feller, S.E. Gawrisch, K. and MacKerell, Jr. A.D. "Polyunsaturated Fatty Acids in Lipid Bilayers: Intrinsic and Environmental Contributions to their Unique Physical Properties," Journal of the American Chemical Society 124: 318-326, 2002.
  73. Foloppe, N. Nilsson, L. and MacKerell, Jr. A.D. "Ab initio conformational analysis of nucleic acid components: Intrinsic energetic contributions to nucleic acid structure and dynamics," Biopolymers 61: 61-76, 2002.
  74. Chen, I-J. Neamati, N. and MacKerell, Jr. A.D. "Structure-Based Inhibitor Design Targeting HIV-1 Integrase," Current Drug Targets - Infectious Disorders 2: 217-234, 2002.
  75. Foloppe, N. Hartmann, B. Nilsson, L. and MacKerell, Jr. A.D. "Intrinsic Conformational Energetics Associated with the Glycosyl Torsion in DNA: a Quantum Mechanical Study," Biophysical Journal 82: 1554-1569, 2002.
  76. Banavali, N.K. and MacKerell, Jr. A.D. "Free Energy and Structural Pathways of Base Flipping in a DNA GCGC containing sequence," Journal of Molecular Biology 319: 141-160, 2002.
  77. Huang, N. and MacKerell, Jr. A.D. "An Ab Initio Quantum Mechanical Study of Hydrogen-Bonded Complexes of Biological Interest," Journal of Physical Chemistry A 106; 7820-7827, 2002.
  78. Andersson, M.P. Uvdal, P. and MacKerell, Jr. A.D. "Fundamental, Binary Combination and Overtone Modes in Methoxy Adsorbed on Cu(100): Infrared Spectroscopy and ab initio Calculations," Journal of Physical Chemistry B 106: 5200-5211, 2002.
  79. 2003

  80. Pan, Y. Huang, N. Cho, S. and MacKerell, Jr. A.D. "Consideration of molecular weight during compound selection in virtual database screening," Journal of Chemical Information and Computer Science 43: 267-272, 2003.
  81. Huang, N. Banavali, N.K. and MacKerell, Jr. A.D. "Protein-facilitated base flipping in DNA by cytosine-5-methyltransferase," Proceedings of the National Academy of Sciences, USA 100: 68-73, 2003.
  82. Chen, W. Wu, H,. Bernard, D. Metcalf, M.D. Deschamps, J. Flippen-Anderson, J. MacKerell, Jr., A.D. and Coop, A. "Rearrangement of 5-Trimethylsilylthebaine on Treatment with L-Selectride: An Efficient Synthesis of (+)-Bractazonine," Journal of Organic Chemistry 68: 1929-1932, 2003.
  83. Bernard, D. Coop, A. and MacKerell, Jr. A.D. "2D Conformationally Sampled Pharmacophore: A Novel Approach to Ligand Based Pharmacophore Development Applied to δ Opioid Agonists and Antagonists," Journal of the American Chemical Society 125: 3103-3107, 2003.
  84. Feig, M. MacKerell, Jr. A.D. and Brooks, III, C.L. "Force field influence on the observation of π-helical protein structures in molecular dynamics simulations," Journal of Physical Chemistry B 107: 2831-2836, 2003.
  85. Lamoureux, G. MacKerell, Jr. A.D. Roux, B. "A simple polarizable model of water based on classical Drude oscillators," Journal of Chemical Physics 119: 5185-5197, 2003.
  86. Pan, Y. and MacKerell, Jr. A.D. "Altered structural fluctuations in duplex RNA versus DNA: A conformational switch involving base pair opening," Nucleic Acids Research 31: 7131-7140, 2003.
  87. 2004

  88. Huang, N. and MacKerell, Jr. A.D. "Atomistic view of base flipping in DNA," Philosophical Transactions of The Royal Society, London, A 362: 1439-1460, 2004.
  89. MacKerell, Jr. A.D. Feig, M. and Brooks, III, C.L. "Improved treatment of the protein backbone in empirical force fields," Journal of the American Chemical Society 126: 698-699, 2004.
  90. Rosen, G.M, Beselman, A. Tsai, P. Pou, S. Mailer, C. Ichikawa, K,. Robinson, B.H. Nielsen, R. Halpern, H. and MacKerell, Jr. A.D. "Influence of Structure on the EPR Spectrum of Spin Trapped Adducts of 5,5-Dimethyl-1-Pyrroline-N-Oxide," Journal of Organic Chemistry 69: 1321-1330, 2004.
  91. Macias, A. Hernandez, R.J. Mehta, A.K. MacKerell, Jr. A.D. Ticku, M.K. and Coop, A. "3-Chloropropanoic acid (UMB66): a ligand for the gamma-hydroxybutyric acid receptor lacking a 4-hydroxyl group," Bioorganic & Medicinal Chemistry 12: 1643-1647, 2004.
  92. Huang, N. Nagarsekar, A. Xia, G. Hayashi, J. and MacKerell, Jr. A.D. "Identification of Non-phosphate containing Small Molecular Weight Inhibitors of the Tyrosine Kinase p56 LCK SH2 Domain via In silico Screening against the pY+3 site," Journal of Medicinal Chemistry 47: 3502-3511, 2004
  93. MacKerell, Jr. A.D. Feig, M. and Brooks, III C.L. "Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations," Journal of Computational Chemistry 25: 1400-1415, 2004.
  94. Patel, S. MacKerell, Jr. A.D. and Brooks, III C.L. "CHARMM fluctuating charge force field for proteins: II Protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model," Journal of Computational Chemistry, 25: 1504-1514, 2004
  95. MacKerell, Jr., A.D. "Empirical Force Fields for Biological Macromolecules: Overview and Issues," Journal of Computational Chemistry 25: 1584-1604, 2004, [DOI]
  96. Horton, J.R. Ratner, G. Banavali, N.K. Huang, H,. Choi, Y. Maier, M.A. Marquez, V.E. MacKerell, Jr. A.D. and Cheng, X. "Caught in the act: visualization of an intermediate in the DNA base-flipping pathway induced by HhaI methyltransferase," Nucleic Acids Research 32: 3877-3886, 2004.
  97. Mason, P.E. Neilson, G.W. Enderby, J.E. Saboungi, M.-L. Dempsey, C.E. MacKerell, Jr. A.D. and Brady, J.W. "The Structure of Aqueous Guanidinium Chloride Solutions," Journal of the American Chemical Society 126: 11462-11470, 2004. [Abstract]
  98. Markowitz, J. Chen, I. Gitti, R. Baldisseri, D.M. Pan, Y. Udan, R. Carrier, F. MacKerell, Jr. A.D. and Weber, D.J. "Identification and Characterization of Small Molecule Inhibitors of the Calcium-Dependent S100B-p53 Tumor Suppressor Interaction," Journal of Medicinal Chemistry 47: 5085-5093, 2004.
  99. Wymore, T. ,Hempel, J. Cho, S.C. MacKerell, Jr. A.D. Nicholas, Jr. H.B. and Deerfield, II D.W. "Molecular recognition of aldehydes by aldehyde dehydrogenase and mechanism of nucleophile activation," Proteins: Structure, Function, and Bioinformatics 57: 758-777, 2004
  100. Pitman, M.C. Frank Suits, F. MacKerell, Jr. A.D. and Feller, S.E. "Molecular Level Organization of Saturated and Polyunsaturated Fatty Acids in a Phosphatidylcholine Bilayer Containing Cholesterol," Biochemistry 43: 15318-15328, 2004.
  101. 2005

  102. Huang, N. and MacKerell, Jr. A.D. "Specificity in Protein-DNA Interactions: Energetic Recognition by the (Cytosine-C5)-methyltransferase from HhaI." Journal of Molecular Biology 345: 265-274, 2005.
  103. Wu, H. Bernard, D. Chen, W. Strahan, G.D. Deschamps, J.R. Parrish, D.A. Lewis, J.W. MacKerell, Jr. A.D. and Coop, A. "Functionalization of the 6,14-bridge of the orvinols. 2. Preparation of 18- and 19-hydroxyl substituted thevinols and their treatment with benzyl bromide," Journal of Organic Chemistry 70: 1907-1910, 2005.
  104. Klauda, J.B. Brooks, B.R. MacKerell, Jr. A.D. Richard M. Venable, R.M. and Pastor, R.W. "An Ab Initio Study on the Torsional Surface of Alkanes and its Effect on Molecular Simulations of Alkanes and a DPPC Bilayer," Journal of Physical Chemistry B 109: 5300-5311, 2005.
  105. MacKerell, Jr. A.D. "Empirical Force Fields for Proteins: Current Status and Future Directions," Annual Reports in Computational Chemistry 1: 91-102, 2005.
  106. Anisimov, V.M. Lamoureux, G. Vorobyov, I.V. Huang, N. Roux, B. and MacKerell, Jr. A.D. "Determination of Electrostatic Parameters for a Polarizable Force Field Based on the Classical Drude Oscillator," Journal of Chemical Theory and Computation 1: 153-168, 2005.
  107. Pan, Y. Priyakumar, D. and MacKerell, Jr. A.D. "Conformational Determinants of Tandem GU Mismatches in RNA: Insights from molecular dynamics simulations and quantum mechanical calculations," Biochemistry 44: 1433-1443, 2005.
  108. Boresch, S. Leitgeb, M. Beselman, A. MacKerell, Jr. A.D. "Unexpected relative aqueous solubilities of a phosphotyrosine analogue and two phosphonate derivatives," Journal of the American Chemical Society 127: 4640-4648, 2005.
  109. Wu, H. Thatcher, L.N. Bernard, D. Parrish, D.A. Deschamps, J.R. Rice, K.C. MacKerell, Jr. A.D. and Coop, A. "The Position of Coordination of the Lithium Ion Determines the Regioselectivity of Demethylations of 3,4-Dimethoxymorphinans with L-Selectride," Organic Letters 7: 2531-2534, 2005.
  110. Bernard, D. Coop, A. and MacKerell, Jr. A.D. "Computer-Aided Drug Design: Structure-Activity Relationships of Delta Opioid Ligands." Drug Design Reviews 2: 277-291, 2005.
  111. Hancock, C.N. Macias, A. Lee, E.K. Yu, S.Y. MacKerell, Jr. A.D. and Shapiro, P. "Identification of novel extracellular signal-regulated kinase (ERK) docking domain inhibitors," Journal of Medicinal Chemistry 48: 4586-4595, 2005.
  112. Macias, A.T. and MacKerell, Jr. A.D. "CH/pi Interactions Involving Aromatic Amino Acids: Refinement of the CHARMM Tryptophan Force field," Journal of Computational Chemistry 26: 1452-1463, 2005.
  113. Habtemariam, B. Anisimov, V.M. and MacKerell, Jr. A.D. "Cooperative binding of DNA and CBFβ to the Runt domain of the CBFα studied via MD simulations," Nucleic Acids Research 33: 4212-4222, 2005. [Full Text]
  114. Vorobyov, I.V. Anisimov, V.M. and MacKerell, Jr. A.D. "Polarizable Empirical Force Field for Alkanes Based on the Classical Drude Oscillator Model," Journal of Physical Chemistry B 109: 18988-18999, 2005.
  115. Markowitz, J. MacKerell, Jr. A.D. Carrier, F. Charpentier, T.H. and Weber, D. J. "Design of Inhibitors of S100B," Current Topics in Medicinal Chemistry 5: 1093-1108, 2005.
  116. Bernard, D. Coop, A. MacKerell, Jr. A.D. "Conformationally Sampled Pharmacophore for Peptidic δ Opioid Ligands," Journal of Medicinal Chemistry 48: 7773-7780, 2005.
  117. Macias, A.T. Mia, M.Y. Xia, G. Hayashi, J. and MacKerell, Jr. A.D. "Lead Validation and SAR Development via Chemical Similarity Searching: Application to Compounds Targeting the pY+3 Site of the SH2 Domain of p56 LCK," Journal of Chemical Information and Modeling 45: 1759-1766, 2005.
  118. 2006

  119. Priyakumar, U.D. and MacKerell, Jr. A.D. "Base Flipping in a GCGC Containing DNA Dodecamer: A Comparative Study of the Performance of the Nucleic Acid Force Fields, CHARMM, AMBER and BMS," Journal of Chemical Theory and Computation 2: 187-200, 2006.
  120. Buck, M. Bonnet, S. Pastor, R.W. and MacKerell, Jr. A.D. "Importance of the CMAP correction to the CHARMM22 Protein Force Field: dynamics of hen lysozyme," Biophysical Journal 90: L36-L38, 2006. Online: Dec. 16, 2005. [Full Text]
  121. Lamoureux, G. Harder, E. Vorobyov, I.V. Roux, B. and MacKerell, Jr. A.D. "A polarizable model of water for molecular dynamics simulations of biomolecules," Chemical Physics Letters 418: 245-249, 2006.
  122. Priyakumar, U.D. and MacKerell, Jr. A.D. "NMR Imino Proton Exchange Experiments on Duplex DNA Primarily Monitor the Opening of Purine Bases," Journal of the American Chemical Society (Communication) 128: 678-679, 2006.
  123. Hancock, C.N. Macias, A. MacKerell, Jr. A.D. and Shapiro, P. "Mitogen Activated Protein (MAP) Kinases: Development of ATP and Non-ATP Dependent Inhibitors," Medicinal Chemistry 2: 213-222, 2006.
  124. Priyakumar, U.D. and MacKerell, Jr. A.D. "Computational Approaches for Investigating Base Flipping in Oligonucleotides," Chemical Reviews 106: 489-505, 2006.
  125. Banavali, N.B. Huang, N. and MacKerell, Jr. A.D. "Conserved Patterns in Backbone Torsional Changes Allow For Single Base Flipping from Duplex DNA with Minimal Distortion of the Double Helix," Journal of Physical Chemistry B 110: 10997-11004, 2006.
  126. Guvench, O. and MacKerell, Jr. A.D. "Quantum Mechanical Analysis of 1,2-Ethanediol Conformational Energetics and Hydrogen Bonding," Journal of Physical Chemistry A 110: 9934-9939, 2006. [Full Text]
  127. Chen, I.-J. Taneja, R. Yin, D. Seo, P.R. Young, D. MacKerell, Jr. A.D. and Polli, J.E. "Chemical Substituent Effect on Pyridine Permeability and Mechanistic Insights from Computational Molecular Descriptors" Molecular Pharmaceutics 3:745-755, 2006.
  128. Harder, E. Anisimov, V.M. Vorobyov, I.V. Lopes, P.E. Noskov, S. MacKerell, Jr. A.D. and Roux, B. "Atomic Level Anisotropy in the Electrostatic Modeling of Lone Pairs for a Polarizable Force Field based on the Classical Drude Oscillator," Journal of Chemical Theory and Computation, 2: 1587-1597. 2006.
  129. Lopes, P.E.M. Murashov, V. Tazi, M. Demchuk, E. and MacKerell, Jr. A.D. "Development of an Empirical Force Field for Silica. Application to the Quartz-Water Interface," Journal of Physical Chemistry B 110: 2782-2792, 2006.
  130. Chen, F. Hancock, C.N. Macias, A.T. Joh, J. Still, K. Zhong, S. MacKerell, Jr. A.D. and Shapiro, P.S. "Characterization of ATP independent ERK inhibitors identified through in silico analysis of the active ERK2 structure," Bioorganic and Medicinal Chemistry Letters 16: 6281-627, 2006.
  131. Macias, A.T. Banavali, N.K. and MacKerell, Jr. A.D. "DNA bending induced by carbocyclic sugar analogs constrained to the north conformation," Biopolymers 8: 438-449, 2006. [Abstract]
  132. 2007

  133. Mayaan, E. Moser, A. MacKerell, Jr. A.D. and York, D.M. "CHARMM force field parameters for simulation of reactive intermediates in native and thio-substituted ribozymes," Journal of Computational Chemistry 28: 495-507, 2007.
  134. Zhong, S. Macias, A.T. and MacKerell, Jr. A.D. "Computational identification of the inhibitors of protein-protein interactions," Current Topics in Medicincal Chemistry 7: 63-82, 2007.
  135. Almond, A. Blundell, C. Higman, V. MacKerell, Jr. A.D. and Day, A. "Using molecular dynamics simulations to provide new insights into protein structure on the nanosecond timescale: comparison with experimental data and biological inferences for the hyaluronan-binding Link module of TSG-6," Journal of Chemical Theory and Computation 3: 1-16, 2007.
  136. Markowitz, J. MacKerell, Jr. A.D. and Weber, D.J. "A search for inhibitors of S100B, a member of the S100 family of calcium-binding proteins," Mini-Reviews in Medicinal Chemistry 7: 609-616, 2007.
  137. Vorobyov, I.V. Anisimov, V.M. Greene, S. Venable, R.M. Moser, A. Pastor, R.W. and MacKerell, Jr. A.D. "Additive and Classical Drude Polarizable Force Fields for Linear and Cyclic Ethers," Journal of Chemical Theory and Computation 3: 1120-1133, 2007.
  138. Lopes, P. Lamoureux, G. Roux, B. and MacKerell, Jr. A.D. "Polarizable Empirical Force Field for Aromatic Compounds Based on the Classical Drude Oscillator," Journal of Physical Chemistry B 111: 2873-2885, 2007.
  139. Woodcock, H.L. Moran, D. Pastor, R.W. MacKerell, Jr. A.D. and Brooks, B.R. "Ab initio modeling of glycosyl torsions and anomeric effects in a model carbohydrate: 2-Ethoxy Tetrahydropyran," Biophysical Journal 93: 1-10, 2007.
  140. Guvench, O. Qu, C.K. MacKerell, Jr. A.D. "Tyr66 acts as a conformational switch in the closed-to-open transition of the SHP-2 N-SH2-domain phosphotyrosine-peptide binding cleft," BioMed Central (BMC) Structural Biology 7: 14, 2007.
  141. Bernard, D. Coop, A. and MacKerell, Jr. A.D. "Quantitative Conformationally Sampled Pharmacophore for δ Opioid Ligands: Reevaluation of Hydrophobic Moieties Essential for Biological Activity," Journal of Medicinal Chemistry 50: 1799-1809, 2007.
  142. Furci, L.M. Lopes, P. Eakanunkul, S. Zhong, S. MacKerell, Jr. A.D. Wilks, A. "Inhibition of the Bacterial Heme Oxygenases from Pseudomonas aeruginosa (pa-HO) and Neisseria meningitidis (nm-HO): A Novel Antimicrobial Target," Journal of Medicinal Chemistry 50: 3804-3813, 2007.
  143. Anisimov, V.M. Vorobyov, I.V. Roux, B. and MacKerell, Jr. A.D. "Polarizable empirical force field for the primary and secondary alcohol series based on the classical Drude model," Journal of Chemical Theory and Computation 3: 1927-1946, 2007.
  144. Zhong, S. and MacKerell, Jr. A.D. "Binding Response: A Descriptor for Selecting Ligand Binding Site on Protein Surfaces," Journal of Chemical Information and Modeling 47: 2303-2315, 2007.
  145. Xie, W. Pu, J, MacKerell, Jr. A.D. and Gao, J. "Development of a polarizable intermolecular potential function (PIPF) for liquid amides and alkanes," Journal of Chemical Theory and Computation 3: 1878-1889, 2007.
  146. Thomas, J.L. Tobias, D.J. and MacKerell, Jr. A.D. "Direct Comparisons of Experimental and Calculated Neutron Structure Factors of Pure Solvents as a Method for Force Field Validation," Journal of Physical Chemistry B 111: 12941-12944, 2007.
  147. 2008

  148. Li, L. Vorobyov, I.V. MacKerell, Jr. A.D. Allen, T.W. "Is arginine charged in a membrane?" Biophysical Journal (Letter) 94: L11-L13, 2008.
  149. Priyakumar, U.D. and MacKerell, Jr. A.D. "Atomic detail investigation of the structure and dynamics of DNA·RNA hybrids: A molecular dynamics study," Journal of Physical Chemistry B 112: 1515-1524, 2008.
  150. Guvench, O. and MacKerell, Jr. A.D. "Automated conformational energy fitting for force-field development," Journal of Molecular Modeling 14: 667-679, 2008.
  151. Chen, X. Zhong, S. Zhu, X. Dziegielewska, B. Ellenberger, T. Wilson, G.M, MacKerell, Jr. A.D. and Tomkinson, A.E. "Rational Design of Human DNA Ligase Inhibitors that Target Cellular DNA Replication and Repair," Cancer Research 68: 3169-3177, 2008. PMCID: PMC2734474
  152. Harder, E. Anisimov, V.M. Whitfield, T. MacKerell, Jr. A.D. and Roux, B. "Understanding the Dielectric Properties of Liquid Amides from a Polarizable Force Field," Journal of Physical Chemistry B 112: 3509-3521, 2008. PMID: 18302362
  153. MacKerell, Jr. A.D. and Nilsson, L. "Molecular dynamics simulations of nucleic acid-protein complexes," Current Opinions in Structural Biology 18: 194-199, 2008. NIHMSID197576
  154. Guvench, O. Greene, S.N. Kamath, G. Brady, J.W. Venable, R.M. Pastor, R.W. and MacKerell, Jr. A.D. "Additive empirical force field for hexopyranose monosaccharides," Journal of Computational Chemistry 29: 2543-2564, 2008. NIHMSID 196771
  155. Lee, H. Venable, R.M. MacKerell, Jr. A.D. and Pastor, R.W. "Molecular dynamics studies of polyethylene oxide and polyethylene glycol: Hydrodynamic radius and shape anisotropy," Biophysical Journal 95: 1590-1599, 2008. [Abstract] PMCID: PMC2483782
  156. Yu, W.-M. Guvench, O. MacKerell, Jr. A.D. and Qu. C.-K. "Identification of small molecular weight inhibitors of SHP-2 tyrosine phosphatase via in silico screening combined with experimental assay." Journal of Medicinal Chemistry 51: 7396-7404, 2008. PMCID: PMC2645921
  157. MacKerell, Jr. A.D. Shim, J.-H. and Anisimov, V.M. "Re-evaluation of the reported experimental values of the heat of vaporization of N-methylacetamide." Journal of Chemical Theory and Computation 4: 1307-1312, 2008. [Abstract] NIHMSID197589
  158. Zhong, S. and MacKerell, Jr. A.D. "Pose Scaling: Geometrical Assessment of Ligand Binding Poses," Journal of Theoretical and Computational Chemistry 7: 833-852, 2008.
  159. Acharya, C. Seo, P.R. Polli, J.E. and MacKerell, Jr. A.D. "Computational Model for Predicting Chemical Substituent Effects on Passive Drug Permeability across Parallel Artificial Membranes," Molecular Pharmaceutics 5: 818-828, 2008. [Abstract] PMID: 18710255
  160. Zhong, S. Chen, X. Zhu, X. Dziegielewska, B. Bachman, K.E. Ellenberger, T. Ballin, J.D. Wilson, G.M. Tomkinson, A.E. and MacKerell, Jr. A.D. "Identification and Validation of Human DNA Ligase Inhibitors using Computer-Aided Drug Design," Journal of Medicinal Chemistry 51: 4553-4562, 2008. PMCID: PMC2788817
  161. Charpentier, T.H. Wilder, P.T. Liriano, M.A. Varney, K.M. Pozharski, E, MacKerell, Jr. A.D. Coop, A. Toth, E.A. and Weber, D.J. "Divalent metal ion complexes of S100B in the absence and presence of pentamidine," Journal of Molecular Biology 382: 56-73, 2008. PMCID: PMC2636698
  162. Chen, F. MacKerell, Jr. A.D. Luo, Y. and Shapiro, P. "Using Caenorhabditis elegans as a Model Organism for Evaluating Extracellular Signal-Regulated Kinase Docking Domain Inhibitors," Journal of Cell Communication and Signaling 2: 81-92, 2008. PMCID: PMC2648047
  163. Matthews, M.M. Weber, D.J. Shapiro, P.S. Coop, A. and MacKerell, Jr. A.D. "Inhibition of protein-protein interactions with low molecular weight compounds," Current Trends in Medicinal Chemistry 5: 21-32, 2008. NIHMSID197598
  164. 2009

  165. Lopes, P.E.M. Demchuk, E. and MacKerell, Jr. A.D. "Reconstruction of the (011) Surface on a-Quartz: a semi-classical ab initio Molecular Dynamics Study," International Journal of Quantum Chemistry 109: 50-64, 2009.
  166. Lopes, P.E.M. Lamoureux, G. and MacKerell, Jr. A.D. "Polarizable Empirical Force Field for Nitrogen-containing Heteroaromatic Compounds Based on the Classical Drude Oscillator," Journal of Computational Chemistry 30: 1821-1838, 2009, PMC2704921 [DOI]
  167. MacKerell, Jr. A.D. "Contribution of the intrinsic mechanical energy of the phosphodiester linkage to the relative stability of the A, BI and BII forms of duplex DNA," Journal of Physical Chemistry B 113: 3235-3244, 2009. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2784611/
  168. Harder, E. MacKerell, Jr. A.D. and Roux, B. "Electronic Polarization Effects and the Membrane Dipole Potential," Journal of the American Chemical Society 131: 2760-2761, 2009. PMID: 19199514
  169. Guvench, O. and MacKerell, Jr. A.D. "Computational evaluation of protein - small molecule binding," Current Opinion in Structural Biology 19: 56-61, 2009. PMCID: PMC2671234
  170. González, P.M. Acharya, C. MacKerell, Jr. A.D. and Polli, J.E. "Inhibition Requirements of the human Apical Sodium-dependent Bile acid Transporter (hASBT) using Aminopiperidine Conjugates of glutamyl-Bile Acids," Pharmaceutical Research 26: 1665-1678, 2009. PMID: 19384469
  171. Banavali, N. and MacKerell, Jr. A.D. "Characterizing structural transitions using localized free energy landscape analysis," PLOS One 4: e5525, 2009. [Full Text], PMCID: PMC2678196
  172. Hatcher, E. Guvench, O. and MacKerell, Jr. A.D. "CHARMM Additive All-Atom Force Field for Acyclic Polyalcohols, Acyclic Carbohydrates and Inositol," Journal of Chemical Theory and Computation 5: 1315-1327, 2009. PMCID: PMC2760998
  173. Brooks, B.R. Brooks III, C.L. MacKerell, Jr. A.D. Nilsson, L. Petrella, R. J. Roux, B. Won, Y. Archontis, G. Bartels, C. Boresch, S. Caflisch, A. Caves, L. Cui, Q. Dinner, A.R. Feig, M. Fischer, S. Gao, J. Hodoscek, M. Im, W. Kuczera, K.Lazaridis, T. Ma, J. Ovchinnikov, V. Paci, E. Pastor, R.W. Post, C.B. Pu, J.Z. Schaefer, M. Tidor, B. Venable, R.V. Woodcock, H.L. Wu, X, Yang, W. York, D.M. and Karplus, M. "CHARMM: The biomolecular simulation program," Journal of Computational Chemistry 30: 1555-1614, 2009. PMCID: PMC2810661
  174. Guvench, O. and MacKerell, Jr. A.D. "Computational Fragment-Based Binding Site Identification by Ligand Competitive Saturation," PLoS Computational Biology 5: e1000435, 2009. PMCID: PMC2700966
  175. Charpentier, T.H. Wilder, P.T. Liriano, M.A. Varney, K.M. Zhong, S. Coop, A. Pozharski, E. MacKerell, Jr. A.D. Toth, E.A. and Weber, D.J. "Small Molecules Bound to Unique Sites in the Target Protein Binding Cleft of Calcium-Bound S100B As Characterized by Nuclear Magnetic Resonance and X-ray Crystallography," Biochemistry 48: 6202-6212, 2009. PMCID: PMC2804263
  176. Sorci, L. Pan,, Y. Eyobo, Y. Rodionova, I. Huang, N. Kurnasov, O. Zhong, S. MacKerell, Jr. A.D. Zhang, H. and Osterman, A.L. "Targeting NAD biosynthesis in bacterial pathogens. Structure-based development of inhibitors of nicotinate mononucleotide adenylyltransferase NadD," Chemistry and Biology 16: 849-861, 2009. PMCID: PMC2770502
  177. Lopes, P.E.M. B. Roux, R. MacKerell, Jr. A.D. "Molecular modeling and dynamics studies with explicit inclusion of electronic polarizability. Theory and applications," Theoretical Chemistry Accounts 124: 11-28, 2009, PMC2888514
  178. Hatcher, E. Guvench, O. and MacKerell, Jr. A.D. "CHARMM Additive All-Atom Force Field for Aldopentofuranose Carbohydrates and Fructofuranose," Journal of Physical Chemistry B 113: 12466-76, 2009. PMCID: PMC2741538
  179. Guvench, O. Hatcher, E.R. Venable, R.M. Pastor, R.W. and MacKerell Jr., A.D. "Additive Empirical CHARMM Force Field for glycosyl linked hexopyranoses," Journal of Chemical Theory and Computation 5: 2353-2370, 2009, [DOI], PMC2757763
  180. Burkhard, K. Smith, S. Deshmukh, R. MacKerell, Jr. A.D. and Shapiro, P. "Development of extracellular signal-regulated kinase inhibitors," Current Topics in Medicinal Chemistry 9: 678-89, 2009. PMCID: PMC2835149
  181. Priyakumar, D. Hyeon, C. Thiramuli, D. and MacKerell, Jr. A.D. "Formation of stacking interactions and multiple hydrogen bonds by urea with nucleic acid bases destabilizes RNA," Journal of the American Chemical Society (Communication) 131: 17759-17761, 2009. PMCID: PMC2791195
  182. 2010

  183. Cunningham, C.W. Hom, K. Acharya, C. Wilks, A. MacKerell, Jr. A.D. and Coop, A. "Synthesis and Characterization of a Novel Diels-Alder Adduct of Cocaine," Helvetica Chimica Acta, 93: 220-226, 2010.
  184. Baker, C. and MacKerell, Jr. A.D. "Polarizability Rescaling and atom-based Thole Scaling in the CHARMM Drude Polarizable Force Field for Ethers," Journal of Molecular Modeling 16: 567-576, 2010. PMCID: PMC2818097
  185. Vanommeslaeghe, K. Hatcher, E. Acharya, C. Kundu, S. Zhong, S. Shim, J. E. Darian, E. Guvench, O. Lopes, P. Vorobyov, I. and MacKerell, Jr. A.D. "CHARMM General Force Field (CGenFF): A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields," Journal of Computational Chemistry 31: 671-90, 2010. NIHMSID 196732, PMC2888302, [DOI]
  186. Cerchietti, L.C. Ghetu, A.F. Zhu, X. Da Silva, G.F. Zhong, S. Matthews, M. Bunting, K. Polo, J.M. Farès, C. Arrowsmith, C.H. Yang, S.N. Garcia, M. Coop, A. MacKerell, Jr. A.D., Privé, G.G. Melnick, A. "A small molecule inhibitor of BCL6 kills DLBCL cells in vitro and in vivo," Cancer Cell 17: 400-411, 2010. PMCID: PMC2858395
  187. Priyakumar, U.D. and MacKerell, Jr. A.D. "Role of the Adenine Ligand on the Stabilization of the Secondary and Tertiary Interactions in the Adenine Riboswitch," Journal of Molecular Biology 396: 1422-1438, 2010. PMCID: PMC2824916
  188. Zhu, X. and MacKerell, Jr. A.D. "Polarizable Empirical Force Field for Sulfur-Containing Compounds Based on the Classical Drude Oscillator Model," Journal of Computational Chemistry 12: 2330-2341, 2010. NIHMSID 225436
  189. Yu, H. Whitfield, T.W. Harder, E. Lamoureux, G. Vorobyov, I. Anisimov, V. M. MacKerell, Jr. A.D. and Roux, B. "Simulating Monovalent and Divalent Ions in Aqueous Solution Using a Drude Polarizable Force Field," Journal of Chemical Theory and Computation 6: 774-786, 2010. NIHMSID197625, PMCID: PMC2838399
  190. Baker, C. Lopes, P. Zhu, X. and MacKerell, Jr. A.D. "Accurate Calculation of Hydration Free Energies using the CHARMM Drude Polarizable Force Field," Journal of Chemical Theory and Computation 6: 1181-1198, 2010. NIHMSID184045, PMCID: PMC2853947
  191. Klauda, J.B., Venable, R.M., Freites, J.A., O'Connor, J.W., Tobias, D.J., Mondragon-Ramirez, C., Vorobyov, I., MacKerell, Jr., A.D., and Pastor, R.W. "Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types," Journal of Physical Chemistry B, 114: 7830-7843, 2010, [DOI]
  192. Rais, R. Acharya, C. Tririya, G, MacKerell, Jr. A.D. and Polli, J. "Molecular Switch Controlling the Binding of Anionic Bile Acid Conjugates to hASBT," Journal of Medicinal Chemistry 53: 4749-4760, 2010. PMCID: PMC2891776
  193. Huang, N. Kolhatkar, R. Eyobo, Y. Sorci, L, Osterman, A.L, MacKerell, Jr. A.D. and Zhang, H. "Structures of bacterial NaMN adenylyltransferase in complex with inhibitors: implication for structure based drug design and improvement," Journal of Medicinal Chemistry 53: 5229-5239, 2010. PMCID: PMC2915899
  194. Wilder, P.T. Charpentier, T.H. Liriano, M.A. Gianni, K. Varney, K.M. Pozharski, E. Coop, A. Toth, E.A. MacKerell, Jr. A.D. and Weber, D.J. "In vitro screening and structural characterization of inhibitors of the S100B-p53 interaction," International Journal of High Throughput Screening 1: 109-126, 2010. PMCID: PMC2995924
  195. Semenyuk, A. Darian, E. Liu, J. Majumdar, A. Cuenoud, B. Miller, P. MacKerell,Jr. A.D. and Seidman, M. "Targeting of an interrupted Polypurine:Polypyrimidine sequence in a Triplex forming oligonucleotide containing a novel base analog," Biochemistry 49: 7867-7878, 2010. PMCID: PMC2935506
  196. He, X. Guvench, O. MacKerell, Jr. A.D. and Klein, M.L. "Atomistic Simulation Study of Linear Alkylbenzene Sulfonates at The Water/Air Interface," Journal of Physical Chemistry B 114: 9787-9794, 2010. PMCID: PMC2924668
  197. Raman, P. Guvench, O. MacKerell, Jr. A.D. "CHARMM Additive All-Atom Force Field for Glycosidic Linkages in Carbohydrates Involving Furanoses," Journal of Physical Chemistry B 114: 12981-12994, 2010, [DOI], PMC2958709
  198. West, A.L. St. John, F. Lopes, P.E.M. MacKerell, Jr. A.D. Pozharski, E. and Sarah L.J. and Michel, S.L.J. "Holo-Ni(II)HpNikR is an asymmetric tetramer containing two different nickel binding sites," Journal of the American Chemical Society 132: 14447-14456, 2010. PMCID: PMC2958704
  199. Venable, R.M. Hatcher, E. Guvench, O, MacKerell, Jr. A.D. and Pastor, R.W. "Comparing Simulated and Experimental Translation and Rotation Constants: Range of Validity for Viscosity Scaling," Journal of Physical Chemistry B 114: 12501-12507, 2010. NIHMSID #272317
  200. Rais, R. Acharya, C. MacKerell, Jr. A.D. and Polli, J. "Structural Determinants for Transport Across the Intestinal Bile Acid Transporter Using C-24 Bile Acid Conjugates," Molecular Pharmaceutics 7: 2240-2254, 2010. PMCID: PMC2997912
  201. 2011

  202. Hatcher, E. Säwén, E. Widmalm, G. and MacKerell, Jr. A.D. "Conformational properties of Methyl-maltoside and Methyl α- and β-cellobioside disaccharides," Journal of Physical Chemistry B 115: 597-608, 2011. NIHMSID #258949
  203. Velvadapu, V. Paul, T. Wagh, B. Klepacki, D. Guvench, O. MacKerell, Jr. A.D. and Andrade, R.B. "Desmethyl Macrolides: Synthesis and Evaluation of 4,8,10-Tridesmethyl Telithromycin," ACS Medicinal Chemistry Letters 2: 68-72, 2011. [Abstract]
  204. Yap, J.L. Workikar, S. MacKerell, Jr. A.D. Shapiro, P. and Fletcher, S. "Small-Molecule Inhibitors of the ERK Signalling Pathway: Towards Novel Anticancer Therapeutics," ChemMedChem 6: 38-48, 2011.
  205. Acharya, C. Polli, J. Coop, A. and, MacKerell, Jr. A.D. "Recent Advances in Ligand-Based Drug Design: Relevance and Utility of the Conformationally Sampled Pharmacophore Approach," Current Computer-Aided Drug Design 7: 10-22, 2011. NIHMSID # 230044
  206. Abel, S. Dupradeau, F.-Y. Raman, E.P. MacKerell, Jr. A.D. and Marchi, M. "Molecular Simulations of Dodecyl-β-maltoside Micelles in Water: Influence of Headgroup Conformation and the Force field Parameters," Journal of Physical Chemistry B 115: 487-499, 2011. NIHMSID #261577
  207. Oashi, T. Ringer, A.L. Raman, E.P. and MacKerell, Jr. A.D. "Automated selection of compounds with physicochemical properties to maximize bioavailability and druglikeness," Journal of Chemical Information and Modeling 51: 148-158, 2011.
  208. Baker, C.M. Anisimov, V.M. and MacKerell, Jr. A.D. "Development of CHARMM Polarizable Force Field for Nucleic Acid Bases Based on the Classical Drude Oscillator Model," Journal of Physical Chemistry B 115: 580-596, 2011. NIHMSID #259591
  209. Jiang, W. Hardy, D. Phillips, J. MacKerell, Jr. A.D. Schulten, K. and Roux, B. "High-performance Scalable Molecular Dynamics Simulations of a Polarizable Force Field Based on Classical Drude Oscillators in NAMD," Journal of Physical Chemistry Letters 2: 87-92: 2011.
  210. Boston, S.R. Deshmukh, R. Strome, S. Priyakumar, U.D. MacKerell, Jr. A.D. and Shapiro, P. "Characterization of ERK Docking Domain Inhibitors that Induce Apoptosis by Targeting Rsk-1 and Caspase-9," BMC Cancer 11: 7, 2011. PMCID: PMC3025971
  211. Denning, E.J. Priyakumar, U.D. Nilsson, L. and MacKerell, Jr. A.D. "Impact of 2'-hydroxyl sampling on the conformational properties of RNA: Update of the CHARMM all-atom additive force field for RNA," Journal of Computational Chemistry 32: 1929-1943, 2011, [DOI]
  212. Darian, E. Guvench, O. Yu, B. Qu, C.-K. and MacKerell, Jr. A.D. "Structural mechanism associated with domain opening in gain-of-function mutations in SHP2 phosphatase," Proteins: Structure, Function and Bioinformatics 79: 1573-1588, 2011. NIHMSID #263852
  213. Busby, B. Oashi, T. Willis, C.D. Borzok, M.A. Kontrogianni-Konstantopoulos, A. MacKerell, Jr. A.D. and Bloch, B.J. "Electrostatic Interactions Mediate Binding of Obscurin to Small Ankyrin 1: Biochemical and Molecular Modeling Studies," Journal of Molecular Biology 408: 321-334, 2011.
  214. Ringer, A. L. and MacKerell, Jr. A.D. "Calculation of the Vibrational Stark Effect Using a First-Principles QM/MM Approach," Journal of Physical Chemistry Letters, 2: 553-556, 2011. NIHMSID #275470
  215. Pastor, R.W. and MacKerell, Jr. A.D. "Development of the CHARMM Force Field for Lipids," Journal of Physical Chemistry Letters (Invited Perspective) 2: 1526-1532, 2011.
  216. Raman, E.P. Yu, W. Guvench, O. and MacKerell, Jr. A.D. "Reproducing Crystal Binding Modes of Ligand Functional Groups using Site-Identification by Ligand Competitive Saturation (SILCS) Simulations," Journal of Chemical Information and Modeling 51: 877-896, 2011.
  217. Denning, E.J. and MacKerell, Jr. A.D. "Impact of Arsenic/Phosphorous substitution on the intrinsic conformational properties of the phosphodiester backbone of DNA investigated using ab initio quantum mechanical calculations," Journal of the American Chemical Society (Communication) 133: 5770-5772, 2011.
  218. Shim, J., and MacKerell, A.D., Jr., "Computational ligand-based rational design: Role of conformational sampling and force fields in model development," Med. Chem. Commun., 2: 356-370, 2011, DOI: 10.1039/c1md00044f, PMC3123535
  219. Shim, J., Coop, A. and Alexander D. MacKerell, A.D., Jr. "Consensus 3D Model of μ-Opioid Receptor Ligand Efficacy based on a Quantitative Conformationally Sampled Pharmacophore" Journal of Physical Chemistry B, 115: 7487-7496, 2011, PMC3113728
  220. Jo, S., Song, K.C., Desaire, H., MacKerell, A.D., Jr., and Im, W. "Glycan Reader: Automated Sugar Identification and Simulation Preparation for Carbohydrates and Glycoproteins," Journal of Computational Chemistry, 32, 3135-3141, 2011, PMC3188666
  221. Barr, D., Oashi, T., Burkhard, K., Lucius, S., Samadani, R., Zhang, J., Shapiro, P., MacKerell, A.D., Jr., van der Vaart, A., "The importance of domain closure for the auto-activation of ERK2," Biochemistry, 50: 8038-48, 2011, PMC3172398
  222. Mallajosyula, S.S. and MacKerell, A.D., Jr. "Influence of Solvent and Intramolecular Hydrogen Bonding on the Conformational Properties of O-Linked Glycopeptides," Journal of Physical Chemistry B, 115:11215-11229, 2011, PMC3179525
  223. Guvench, O., Mallajosyula, S.S. Raman, E.P., Hatcher, E. Vanommeslaeghe, K., Foster, T.J., Jamison II, F.W., and MacKerell, A.D., Jr. "CHARMM additive all-atom force field for carbohydrate derivatives and their utility in polysaccharide and carbohydrate-protein modeling," Journal of Chemical Theory and Computing, 7: 3162-3180, 2011, [DOI], PMC3224046
  224. Fribourg, M., Moreno, J.L., Provasi, D., Holloway, T., Mahajan, R., Park, G., Baki, L., Adney, S.K., Hatcher, C., Ruta, J.D., Albizu, L., Li, Z., Shim, J., Fabiato, A., MacKerell, A.D., Jr., Brezina, V., Sealfon, S.C., Filizola, M., González-Maeso, J. and Logothetis, D.E., "Decoding the signalling of a GPCR heteromeric complex reveals the mechanism of action of antipsychotic drugs," Cell, 147: 1011-1023, 2011.
  225. Xu, Z., Chen, Y.-W., Battu, A., Wilder, P., Weber, D., Yu, W., MacKerell, A.D., Jr. Chen, L.-M., Chai, K., Johnson, M., Lin, C.-Y., "Targeting zymogen activation to control the matriptase-prostasin proteolytic cascade," Journal of Medicinal Chemistry, 54: 7567-7578, 2011, PMC3214968
  226. 2012

  227. Kolhatkar, V., Diao, L., Acharya, C., MacKerell, A.D., Jr., Polli, J. "Identification of novel non-steroidal compounds as substrates or inhibitors of hASBT," Journal of Pharmaceutical Sciences, 101: 116-126, 2012, DOI: 10.1002/jps.22728
  228. Zhu, X., Lopes, P.E., and MacKerell, A.D., Jr., "Recent developments and applications of the CHARMM force fields," WIRES Computational Molecular Science, 2: 167-185, 2012, DOI: 10.1002/wcms.74, PMC3468154
  229. Hart, K., Foloppe, N., Baker, C.M., Denning, E.J., Nilsson, L. and MacKerell, A.D., Jr., "Optimization of the CHARMM additive force field for DNA: Improved treatment of the BI/BII conformational equilibrium," Journal of Chemical Theory and Computation, 8: 348-362, 2012, [DOI] PMC3285246
  230. Underwood, K., D'Souza, D., Mochin-Peters, M., Pierce, A., Kommineni, S., Choe, M., Bennett, J., Gnatt, A., Habtemariam, B., MacKerell, A., and Passaniti, A. "Regulation of RUNX2 transcription factor-DNA interactions and cell proliferation by Vitamin D3 (cholecalciferol) prohormone activity," Journal of Bone and Mineral Research, 27: 913-925, 2012, 10.1002/jbmr.1504.
  231. Mallajosyula, S.S., Guvench, O., Hatcher, E., MacKerell, A.D., Jr., "CHARMM Additive All-Atom Force Field for Phosphate and Sulfate Linked to Carbohydrates," Journal of Chemical Theory and Computation, 8: 759-776, 2012, DOI: 10.1021/ct200792v, PMC3367516
  232. Yap, J.L., Cao, X., Vanommeslaeghe, A., Jung, K.-Y., Wilder, P.T., Anjan Nan, A., Hom, K., MacKerell, A.D., Jr., Smythe, W.R., and Fletcher, S.,"Relaxation of the rigid backbone of an oligoamide-foldamer-based α-helix mimetic: identification of potent Bcl-xL inhibitors," Organic and Biomolecular Chemistry, 16: 2269-2283, 2012, DOI: 10.1039/c2ob07125h
  233. Denning, E.J. and MacKerell Jr., A.D. "Intrinsic contribution of the 2'-hydroxyl to RNA conformational heterogeneity," Journal of the American Chemical Society, 134: 2800-2806, 2012, PMC3275647, [DOI]
  234. Velvadapu, V., Glassford, I., Lee, M., Paul, T., DeBrosse, C., Klepacki, D., Small, M.C., MacKerell, A.D., Jr., and Andrade, R.B., "Desmethyl Macrolides: Synthesis and Evaluation of 4,10-Didesmethyl Telithromycin," ACS Medicinal Chemistry Letters, 3: 211-215, 2012, PMC3374412
  235. González, P.M., Hussainzada, N., Swaan, P.W., MacKerell Jr., A.D., and Polli, J.E., "Putative irreversible inhibitors of the human sodium-dependent bile acid transporter (hASBT; SLC10A2) support the role of transmembrane domain 7 in substrate binding/translocation," Pharmaceutical Research, 29: 1821-1831, 2012, doi: 10.1007/s11095-012-0706-8.
  236. Willis, C.D., Oashi, T. Busby, B., MacKerell Jr., A.D. and Bloch, R.J. "Hydrophobic Contribution to Binding of Obscurin and Small Ankyrin 1, Molecular Membrane Biology, 29: 36-51, 2012.
  237. Raman, E.P., Vanommeslaeghe, K. and MacKerell Jr., A.D., "Site-Specific Fragment Identification Guided by Single-Step Free Energy Perturbation Calculations." Journal of Chemical Theory and Computation, 8: 3513-3525, 2012, PMC3490637, doi: 10.1021/ct300088r
  238. Maiti, A., Noon, M.S., MacKerell Jr., A.D., Pozharski, E. and Drohat, A.C., "Lesion processing by a repair enzyme is severely curtailed by residues needed to prevent aberrant activity on undamaged DNA," Proceedings of the National Academy of Sciences, 109: 8091-8096, 2012, PMC3361372, doi: 10.1073/pnas.1201010109 Article highlighted in Chemical Research in Toxicology.
  239. Yu, W., Wu, Z., Chen, H., Liu, X., MacKerell Jr., A.D. and Lin, Z. "Comprehensive Conformational Studies of Five Tripeptides and a Deduced Method for Efficient Determinations of Peptide Structures" Journal of Physical Chemistry B., 116: 2269-2283, 2012, PMC3288331, DOI: 10.1021/jp207807a, PMC3288331
  240. Foster, T.J., MacKerell Jr., A.D. and Guvench, O. "Balancing Target Flexibility and Target Denaturation in Computational Fragment-Based Inhibitor Discovery," Journal of Computational Chemistry, 33:1880-91, 2012, PMC3438888
  241. Stavitskaya, L., Shim, J., Healy, J.R., Matsumoto, R.R., MacKerell Jr., A.D., Coop, A. "Deconstructing 14-phenylpropyloxymetopon: minimal requirements for binding to mu opioid receptors," Bioorganic & Medicinal Chemistry, 20: 4556-4563, 2012.
  242. Zhu, X., Shim, J., Lopes, P.E.M., and MacKerell Jr., A.D. "Intrinsic energy landscapes of amino acid side chains," Journal of Chemical Information and Modeling, 52:1559-1572, 2012, PMC3398815
  243. Yu, W., He, X., Vanommeslaeghe, K. and MacKerell, A.D., Jr., "Extension of the CHARMM General Force Field to Sulfonyl-Containing Compounds and Its Utility in Biomolecular Simulations," Journal of Computational Chemistry, 33: 2451-2468, 2012, doi: 10.1002/jcc.23067, PMC3477297
  244. Best, R.B., Zhu, X., Shim, J., Lopes, P.E.M., Mittal, J., Feig, M., and MacKerell Jr., A.D. "Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone phi, psi and side-chain chi1 and chi2 dihedral angles," Journal of Chemical Theory and Computation, 8: 3257-3273, 2012, [DOI] PMC3549273
  245. Best, R.B., Mittal, J., Feig, M., and MacKerell Jr., A.D., "Inclusion of many-body effects in the additive CHARMM protein CMAP potential results in enhanced cooperativity of -helix and β-hairpin formation, Biophysical Journal, 103, 1045-1051, 2012, PMC3433603
  246. Petty, A., Myshkin, E., Qin, H., Guo, H., Miao, H., Tochtrop, G.P., Hsieh, J.-T., Page, P., Liu, L., Lindner, D.J., Acharya, C., MacKerell, A.D., Jr. Ficker, E., Song, J., and Wang, B. A Small Molecule Agonist of EphA2 Receptor Tyrosine Kinase Inhibits Tumor Cell Migration in vitro and Prostate Cancer Metastasis in vivo," PLoS One, 7: e42120., 2012, PMC3419725.
  247. Wagh, B., Paul, T., Glassford, I., DeBrosse, C., Klepacki, D., Small, M.C., MacKerell, A.D., Jr., and Andrade, R.B.,"Desmethyl Macrolides: Synthesis and Evaluation of 4,8-Didesmethyl Telithromycin," ACS Medicinal Chemistry Letters, 3:1013-1018, 2012, PMC3763958, DOI: 10.1021/ml200254h.
  248. McKnight, Laura; Raman, E.; Bezawada, Padmavani; Kudrimoti, Sucheta; Wilder, Paul; Hartman, Kira; Toth, Eric; Coop, Andrew; MacKerell, Alexander; Weber, David "Structure-Based Discovery of a Novel Pentamidine-Related Inibitor of the Calcium-Binding Protein S100B," ACS Medicinal Chemistry Letters, 3: 975-979, 2012, DOI: 10.1021/ml300166s, PMC3524579
  249. Vanommeslaeghe, K., and MacKerell Jr., A.D., "Automation of the CHARMM General Force Field (CGenFF) I: bond perception and atom typing," Journal of Chemical Informationa and Modeling, 52: 3144-3154, 2012, DOI: 10.1021/ci300363c, PMC3528824
  250. Vanommeslaeghe, K., Raman, E.P., and MacKerell Jr., A.D., "Automation of the CHARMM General Force Field (CGenFF) II: Assignment of bonded parameters and partial atomic charges, Journal of Chemical Informationa and Modeling, 52: 3155-3168, 2012, DOI: 10.1021/ci3003649, PMC3528813
  251. 2013

  252. Jain, V., Hilton, B., Lin, B., Patnaik, S., Liang, F., Darian, E., Zou, Y., MacKerell Jr., A.D., and Cho, B.P. "Unusual sequence effects on nucleotide excision repair of arylamine lesions: DNA bending/distortion as a primary recognition factor," Nucleic Acids Research, 41: 869-880, 2013, PMC3553991
  253. Shim, J., Zhu, X., Best, R.B., and MacKerell Jr., A.D. "(Ala)4-X-(Ala)4 as a model system for the optimization of the χ1 and χ2 amino acid side chain dihedral empirical force field parameters." Journal of Computational Chemistry, 34: 593-603, 2013, doi: 10.1002/jcc.23178, PMC3570682
  254. Luo, Y., Jiang, W., Yu, H., MacKerell, A.D., Jr., and Roux, B., "Simulation study of ion pairing in concentrated aqueous salt solutions with a polarizable force field," Faraday Discussions, 160, 135 - 149, 2013, DOI: 10.1039/C2FD20068F, PMC3695446
  255. Yu, W., Lopes, P.E.M., Roux, B., and MacKerell, A.D., Jr., "Six-site Polarizable Model of Water Based on the Classical Drude Oscillator" Journal of Chemical Physics, 138, 034508 2013; http://dx.doi.org/10.1063/1.4774577, PMC3562330
  256. Xue, F., MacKerell, A.D., Jr., Heinzl, G., Mbatia, H., and Hom, K. "Room Temperature Catalyst-Free Knoevenagel Condensation: Facile Access to Isatinylidenerhodanines," Tetrahedron Letters, 54, 1700-1703, 2013
  257. Nagagarajan, S., Xue, F., and MacKerell, A.D., Jr. "Impact of substrate protonation and tautomerization states on interactions with the active site of Arginase I," Journal of Chemical Information and Modeling, 53: 452-460, 2013, PMC3590304
  258. McDonald, A.R., Elizabeth J. Denning, E.J, and MacKerell, A.D., Jr. "Impact of geometry optimization on base-base stacking interaction energies in the canonical A- and B-forms of DNA," Journal of Physical Chemistry A, 117: 1560-1568, 2013, PMC3579007.
  259. Hom, K., Heinzl, G.A., Eakanunkul, S., Lopes, P.E.M., Xue, F., MacKerell, A.D., Jr., and Angela Wilks, A., "Small Molecule Antivirulents Targeting the Iron-Regulated Heme Oxygenase (HemO) of P. aeruginosa," Journal of Medicinal Chemistry, 56: 2097-2109, 2013, PMC3643010
  260. Jung, K.-Y., Samadani, R., Chauhan, J., Nevels, K., Yap, J.L., Zhang, J., Worlikar, S., Ensey, M., Shukla, S, Salmo, R., Heinzl, G., Gordon, C., Dukes, T., Lanning, M.E., MacKerell, A.D., Jr., Shapiro, P., and Fletcher, S. "Structural Modifications of (Z)-3-(2-aminoethyl)-5-(4-ethoxybenzylidene)thiazolidine-2,4-dione that Improve Selectivity for Inhibiting Melanoma Cells Containing Active ERK Signaling," Organic & Biomolecular Chemistry, 11: 3706-3732, 2013, PMC3663054
  261. Mallajosyula, S.S., Adams, K.M., Barchi, J.J., and MacKerell, A.D., Jr. "Conformational determinants of the activity of Antiproliferative factor glycopeptide." Journal of Chemical Information and Modeling, 53: 1127-1137 2013, PMC3690088, [DOI]
  262. Cao, X., Yap, J.L., Newell-Rogers, M.K., Peddaboina, C., Hua, J., Papaconstantinou, H.T., Jupitor, D., Rai, A., Jung, K.-Y., Tubin, R.P., Yu, W., Vanommeslaeghe, K., Wilder, P.T., MacKerell, A.D., Jr., Fletcher, S., and Smythe, W.R., "The novel BH3 α-helix mimetic JY-1-106 induces apoptosis in a subset of cancer cells (lung cancer, colon cancer and mesothelioma) by disrupting Bcl-xL and Mcl-1 protein-protein interactions with Bak," Molecular Cancer, 12:42, 2013, PMC3663763.
  263. He, X., Lopes, P.E.M., and MacKerell, A.D., Jr., "Polarizable Empirical Force Field for Acyclic Poly-Alcohols Based on the Classical Drude Oscillator," Biopolymers, 99: 724-738, 2013, doi: 10.1002/bip.22286, NIHMSID #546767
  264. Lakkaraju, K.S. Xue, F., Faden, A., and MacKerell, A.D., Jr., "Estimation of ligand efficacies of metabotropic glutamate receptors from conformational forces obtained from molecular dynamics simulations," Journal of Chemical Information and Modeling, 53: 1337-1349, 2013, PMC3693859
  265. Small, M., Andrade, R., and MacKerell, A.D., Jr., "Impact of Ribosomal Modification on the Binding of the Antibiotic Telithromycin using a Combined Grand Canonical Monte Carlo/Molecular Dynamics Simulation Approach," PLoS Computational Biology, 9: e1003113, 2013, PMC3681621, doi:10.1371/journal.pcbi.1003113
  266. Yu, B., Liu, W., Yu, W.-M., Loh, M., Alter, S., Guvench, O., MacKerell, A.D., Jr., Tang, L.-D., and Qu, C.-K., "Targeting Protein Tyrosine Phosphatase SHP2 for the Treatment of PTPN11-Associated Malignancies," Molecular Cancer Therapeutics, 12:1738-1748. doi: 10.1158/1535-7163, PMC3769526
  267. Sandineni, A., Lin, B., MacKerell, A.D., Jr. and Cho, B.P., "Structure and thermodynamic insights on acetylaminofluorene-modified deletion DNA duplexes as models for frameshift mutagenesis," Chemical Research in Toxicology, 26: 937-951, 2013, PMC3733349
  268. Huang, J., and MacKerell, A.D., Jr. "CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data," Journal of Computational Chemistry, 34: 2135-2145, 2013, PMC3800559
  269. Healy, J., Bezawada, P., Shim, J., MacKerell, A.D., Jr., Coop, A., and Matsumoto, R. "Synthesis, Modeling and Pharmacological Evaluation of UMB 425, a Mixed μ Agonist/δ Antagonist Opioid Analgesic with Reduced Tolerance Liabilities," ACS Chemical Neuroscience, 4:1256-1266, 2013, PMC3778426, [DOI]
  270. Jung, K.-Y., Vanommeslaeghe, K., Lanning, M., Yap, J., Gordon, C., Wilder, P., MacKerell, A.D., Jr., and Fletcher, S., "Amphipathic α-Helix Mimetics Based on a 1,2-Diphenylacetylene Scaffold," Organics Letters, 15: 3234-3237, 2013, PMC3663054
  271. He, X., Hatcher, E., Eriksson, L., Widmalm, G., and MacKerell, A.D., Jr. "Bifurcated Hydrogen Bonding and Asymmetric Fluctuations in a Carbohydrate Crystal Studied via X-ray Crystallography and Computational Analysis," Journal of Physical Chemistry B, 117: 7546-7553, 2013, PMC3771504
  272. Shim, J., Coop, A., and MacKerell, A.D., Jr. "Molecular Details of the Activation of the µ Opioid Receptor," Journal of Physical Chemistry B, 117; 7907-7917, 2013, PMC3735350
  273. Lin, B., Lopes, P.E.M., Roux, B., and MacKerell, A.D., Jr., "Kirkwood-Buff Analysis of Aqueous N-Methylacetamide and Acetamide Solutions Modeled by the CHARMM Additive and Drude Polarizable Force Fields," Journal of Chemical Physics, 139: 084509, 2013, PMC3772949
  274. Chowdhary, J., Harder, E., Lopes, P.E.M., MacKerell, Jr., A.D, and Roux, B., "A Polarizable Model for Phosphatidylcholine-Containing Biological Membranes," Journal of Physical Chemistry B.,117: 9142-9160, 2013. PMC3799809
  275. Jain, V., Hilton, B., Lin, B., Jain, A., MacKerell, A.D., Jr., Zou, Y., and Cho, B., "Structural and Thermodynamic Insight into Escherichia coli UvrABC-Mediated Incision of Cluster Diacetylaminofluorene Adducts on the NarI Sequence," Chemical Research in Toxicology, 26: 1251-1262, 2013, PMC3917139
  276. Raman, E.P., and MacKerell, A.D., Jr., "Rapid estimation of hydration thermodynamics of macromolecular regions," Journal of Chemical Physics, 139: 055105, 2013, PMC3751957
  277. Hatzi, K.; Jiang, Y.; Huang, C.; Garrett-Bakelman, F.; Gearhart, M. D.; Giannopoulou, E. G.; Zumbo, P.; Kirouac, K.; Bhaskara, S.; Polo, J. M., Kormaksson, M., MacKerell, A.D., Jr., Xue, F., Mason, C.E., Hiebert, S.W., Gilbert G. Prive, G.G., Cerchietti, L., Bardwell, V.J., Elemento, O., and Melnick, A. "A Hybrid Mechanism of Action for BCL6 in B Cells Defined by Formation of Functionally Distinct Complexes at Enhancers and Promoters," Cell Reports, 4, 1-11, 2013, [DOI], PMC3854650
  278. Denning, E., Thirumali, D., MacKerell, A.D., Jr., "Protonation of Trimethylamine N-Oxide (TMAO) is required for stabilization of RNA tertiary structure," Biophysical Chemistry, 184: 8-16, 2013. [DOI], PMC3842377
  279. Lin, B., He, X., and MacKerell, A.D., Jr., "A Comparative Kirkwood-Buff Study of Aqueous Methanol Solutions Modeled by the CHARMM Additive and Drude Polarizable Force Fields," Journal of Physical Chemistry B, 117: 10572-10580, 2013, [DOI], PMC3787518
  280. Wagh, B., Paul, T., DeBrosse, C., Klepacki, D., Small, M.C., MacKerell, A.D., Jr., and Andrade, R.B."Desmethyl Macrolides: Synthesis and Evaluation of 4,8,10-Tridesmethyl Cethromycin," ACS Medicinal Chemistry Letters, 4: 1114-1118, 2013, [DOI], PMC3901159
  281. Varney, K., Bonvin, A.M.J.J., Yu, W., Ateh, E., Oashi, T., Huang, J., Diepeveen-de Buin, M., Bryant, J. Breukink, E., MacKerell, A.D., Jr., and de Leeuw, E., "Turning Defense into Offense: Development of Defensin Mimetics as Novel Antibiotics targeting Lipid II," PLoS Pathogens, 9: e1003732, 2013, [DOI], PMC3820767
  282. Sabit, H., Mallajosyula, S.S., MacKerell, A.D., Jr., and Swaan P.W. "Transmembrane Domain II of the Human Bile Acid Transporter SLC10A2 Coordinates Sodium Translocation," Journal of Biological Chemistry, 288: 32349-32404, 2013, [DOI], PMC3820874
  283. Lopes, P.E.M., Huang, J., Shim, J., Luo, Y., Li, H., Roux, B., and MacKerell, A.D., Jr., "Polarizable Force Field for Peptides and Proteins based on the Classical Drude Oscillator," Journal of Chemical Theory and Computation, 2013, 9: 5430-5449 [DOI], PMC3896220
  284. Raman, E.P., Yu, W., Lakkaraju, S.K., and MacKerell, A.D., Jr., "Inclusion of multiple fragment types in the Site Identification by Ligand Competitive Saturation (SILCS) approach," Journal of Chemical Information and Modeling, 53: 3384-3398, 2013, [DOI], PMC3947602
  285. 2014

  286. Vanommeslaeghe, K., Guvench, O., and MacKerell, A.D., Jr., "Molecular Mechanics," in "Advances in Computational Structure Based Drug Discovery", special issue of Current Pharmaceutical Design, In Press, 2014, NIHMSID #579207
  287. Oyer, J.A., Huang, X., Zheng, Y., Shim, J., Ezponda, T., Allegretta, M., Okot-Kotber, C.I., Patel, J.P., Melnick, A., Levine, R.L., Ferrando, MacKerell, A.D., Jr., Kelleher, N.L., Licht, J.D., and Popovic, R., "Point mutation E1099K in MMSET/NSD2 enhances its methyltranferase activity and leads to altered global chromatin methylation in lymphoid malignancies," Leukemia, 28: 198-201, 2014. doi: 10.1038/leu.2013.204, PMC3888226
  288. Sun, X., Rai, R., Deschamps, J.R., MacKerell, A.D., Jr., Faden, A.I., and Fengtian Xue, "Boc-protected 1-(3-oxocycloalkyl)ureas via a one-step Curtius rearrangement: mechanism and scope," Tetrahedron Letters, 2014, 55, 1905-1908. [DOI]
  289. Yu, W., Lakkaraju, S.K., Raman, E.P., and MacKerell, A.D., Jr., "Site-Identification by Ligand Competitive Saturation (SILCS) Assisted Pharmacophore Modeling," Journal of Computer-Aided Molecular Design, 2014, 28: 491-507. [DOI], PMC4048638
  290. Patel, D.S., Pendrill, R., Mallajosyula, S.S., Widmalm, G.* and MacKerell, A.D., Jr.*, "Conformational Properties of α- or β-(1→6)-linked Oligosaccharides: Hamiltonian Replica Exchange MD Simulations and NMR Experiments," Journal of Physical Chemistry B., 2014, 118: 2851-2871. [DOI], PMC3979472
  291. Kumar, P., Bojarowski, S.A., Jarzembska, K.N., Domagala, S., Vanommeslaeghe, K., MacKerell, A.D., Jr., and Dominiak, P.A., "A comparative study of transferable aspherical pseudoatom databank and classical force fields for predicting electrostatic interactions in molecular dimers," Journal of Chemical Theory and Computation, 2014, 10: 1652-1664. [DOI], PMC3985931
  292. Savelyev, A. and MacKerell, A.D., Jr., "All-Atom Polarizable Force Field for DNA Based on the Classical Drude Oscillator Model," Journal of Computational Chemistry, 2014, 35: 1219-1239, PMC4075971 [DOI]
  293. Lakkaraju, S.K., Raman, E.P., Yu, W., and MacKerell, A.D., Jr., "Sampling of Organic Solutes in Aqueous and Heterogeneous Environments Using Oscillating Excess Chemical Potentials in Grand Canonical-like Monte Carlo-Molecular Dynamics Simulations", Journal of Chemical Theory and Computation, 10: 2281-2290, 2014. [DOI]
  294. Lemkul, J.A., Savelyev, A., and MacKerell, A.D., Jr., "Induced Polarization Influences the Fundamental Forces in DNA Base Flipping," Journal of Physical Chemistry Letters, 2014, 5: 2077-2083. [DOI] [ACS LiveSlides]
  295. Venable, R.M., Sodt, A.J., Rogaski, B., Rui, H., Hatcher, E., MacKerell, A.D., Jr., Pastor, R.W. and Klauda, J.B. "CHARMM All-Atom Additive Force Field for Sphingomyelin: Elucidation of Hydrogen Bonding and of Positive Curvature," Biophysical Journal, 2014, 107: 134-145. [DOI], PMC4119286
  296. Savelyev, A. and MacKerell, A.D., Jr., "Balancing the interactions of ions, water and DNA in the Drude polarizable force field," Journal of Physical Chemistry B, 2014, 118: 6742-6757 [DOI], PMC4064693
  297. Li, T., Yang, D., Zhong, S., Thomas, J.M., Xue, F., Liu, J., Kong, L., Voulalas, P., Hassan, H.E., Park, J.-S., MacKerell, A.D., Jr. and Smith, W., "Novel LRRK2 GTP-binding inhibitors reduced degeneration in Parkinson’s disease cell and mouse models," Human Molecular Genetics, 2014, 23: 6212-6222. [DOI]
  298. Glassford, I., Miseon, L., Wagh, B., Velvadapu, V., Paul, T., Sandelin, G., DeBrosse, C., Klepacki, D., Small, M.C., MacKerell, A.D., Jr., and Andrade, R.B.," Desmethyl Macrolides: Synthesis and Evaluation of 4-Desmethyl Telithromycin," ACS Medicinal Chemistry Letters, 2014, 5, 1021-1026. [DOI], PMC4160760
  299. Huang, J. and MacKerell, A.D., Jr., "Induction of peptide bond dipoles drives cooperative helix formation in the (AAQAA)3 peptide," Biophysical Journal, 2014, 107: 991-997. [DOI], PMC4142245
  300. Huang, J., Lopes, P.E.M., Roux, B. and MacKerell, A.D., Jr., "Recent Advances in Polarizable Force Fields for Macromolecules: Microsecond Simulations of Proteins Using the Classical Drude Oscillator Model," Journal of Physical Chemistry Letters, 2014, 5: 3144-3150. [DOI], PMC4167036
  301. Mallajosyula, S., Vanommeslaeghe, K., and MacKerell, A.D., Jr., "Perturbation of Long-Range Water Dynamics as the Mechanism for the Antifreeze Activity of Antifreeze Glycoprotein," Journal of Physical Chemistry B, 2014 118: 11696-11706. [DOI], PMC4191590
  302. Kern, N.R., Lee, H.S., Wu, E.L., Vanommeslaeghe, K., MacKerell, A.D., Jr., Klauda, J.B., Jo, S., and Im, W., "Lipid-Linked Oligosaccharides in Membranes Sample Conformations that Facilitate Binding to Oligosaccharyltransferase," Biophysical Journal, 2014, 107: 1885-1895. [DOI], PMC4213670
  303. 2015

  304. Patel, D.S., He, X., and MacKerell, A.D., Jr., "Polarizable Empirical Force Field for Hexopyranose Monosaccharides based on the Classical Drude Oscillator," Journal of Physical Chemistry B., 2015, 119: 637-652, [DOI], PMC4143499
  305. Vanommeslaeghe, K., and MacKerell, A.D., Jr., "CHARMM additive and polarizable force fields for biophysics and computer-aided drug design," Biochimica et Biophysica Acta: General Subjects, 2015, 1850: 861-871. [DOI], NIHMSID626201
  306. Savelyev, A., and MacKerell, A.D., Jr., "Differential Impact of the Monovalent Ions Li+, Na+, K+ and Rb+ on DNA Conformational Properties," Journal of Physical Chemistry Letters, 6: 212-216, 2015, [DOI], PMC4285411
  307. Yang, M., and MacKerell, A.D., Jr., "Conformational Sampling of Oligosaccharides Using Hamiltonian Replica Exchange with Two-Dimensional Dihedral Biasing Potentials and the Weighted Histogram Analysis Method (WHAM)," Journal of Chemical Theory and Computation, 11: 788Ð799, 2015, [DOI], PMC4334390
  308. Yu, W., Lakkaraju, S.K., Raman, E.P., Fang, L., and MacKerell, A.D., Jr., "Pharmacophore modeling using Site-Identification by Ligand Competitive Saturation (SILCS) with multiple probe molecules," Journal of Chemical Information and Modeling, 55: 407-420, 2015, [DOI], PMC4339487
  309. Raman, E.P. and MacKerell, A.D., Jr., "Spatial Analysis and Quantification of the Thermodynamic Driving Forces in Protein-Ligand Binding: Binding Site Variability," Journal of the American Chemical Society, 137: 2608-2621, 2015, [DOI], PMC4342289
  310. Kasavajhala, K., Bikkina, S., Patil, I., MacKerell, A.D., Jr., and Priyakumar, U.D.,"Dispersion Interactions between Urea and Nucleobases Contribute to the Destabilization of RNA by Urea in Aqueous Solution," Journal of Physical Chemistry B, 119: 3755-3761, 2015, [DOI], PMC4352126
  311. Fletcher, S.F., Yu, W., Huang, J., Kwasny, S.M., Chauhan, J., Opperman, T.J., MacKerell, A.D., Jr., deLeeuw, E.P.H. "Structure-Activity Relationships of a Small-Molecule Lipid II inhibitor," Drug Design, Development and Therapy, 9: 2383-2394, 2015, [DOI], PMC4422293
  312. Lakkaraju, S.K., Yu, W., Raman, E.P., Hershfeld, A.V., Fang, L., Deshpande, D.A., and MacKerell, A.D., Jr., "Mapping Functional Group Free Energy Patterns at Protein Occluded Sites: Nuclear Receptors and G-Protein Coupled Receptors," Journal of Chemical Information and Modeling, 55: 700-708, 2015, [DOI], PMC4372819
  313. Samadani, R., Zhang, J., Brophy, A., Oashi, T., Priyakumar, U.D., Raman, E.P., St John, F.J., Jung, K.-Y., Fletcher, S., Pozharski, E., MacKerell, A.D., Jr.,* and Shapiro, P.,* "Small Molecule Inhibitors of ERK-mediated Immediate Early Gene Expression and Proliferation of Melanoma Cells Expressing Mutated BRaf," Biochemical Journal, 467: 425-438, 2015, [DOI], PMC4643458
  314. Vanommeslaeghe, K., and MacKerell, A.D., Jr., "Robustness in the fitting of Molecular Mechanics parameters," Journal of Computational Chemistry, 36: 1083-1101, 2015, [DOI], PMC4412823
  315. He, X., Lakkaraju, S.K., Hanscom, M., Zhao, Z., Wu, J., Stoica, B., MacKerell, A.D., Jr., Faden, A.I. and Xue, F., "Acyl-2-aminobenzimidazoles: a novel class of neuroprotective agents targeting mGluR5," Bioorganic and Medicinal Chemistry, 23: 2211-2220, 2015, [DOI],PMC4697443
  316. Savelyev, A., and MacKerell, A.D., Jr., "Competition among Li+, Na+, K+ and Rb+ Monovalent Ions for DNA in Molecular Dynamics Simulations using the Additive CHARMM36 and Drude Polarizable Force Fields," Journal of Physical Chemistry B, 119: 4428-4440, 2015, [DOI], PMC4378841
  317. Mistry, P., Laird, M.H.W., Schwarz,, R.S., Greene, S., Dyson, T., Snyder, G.A., Xiao, T.S., Chauhan, J., Fletcher, S., Toshchakov, V.Y., MacKerell, A.D., Jr.,* and Vogel, S.N.,* "Inhibition of TLR2 Signaling by Novel Small Molecule Inhibitors Targeting a Pocket within the TLR2 TIR Domain," Proceedings of the National Academy of Sciences, USA, 112: 5455Ð5460, 2015, [DOI], PMC4418912
  318. Lakkaraju, S.K., Mbatia, H., Hanscom, M., Zhao, Z., Wu, J., Stoica, B., MacKerell, A.D., Jr., Faden, A.I. and Xue, F., "Cyclopropyl-containing positive allosteric modulators of metabotropic glutamate receptor subtype 5," Bioorganic and Medicinal Chemistry, 25: 2275-2279, 2015, [DOI], PMC4690453
  319. Mei, Y., Wang, Y., Kumari, P., Shetty, A.C., Clark, D., Gable, T., MacKerell, A.D., Jr., Ma, M.Z., Weber, D., Edelman, M., Mao, L., "piRNA-L-163 interacts with p-ERM proteins in human somatic cells and modulates ERMÕs functional activities," Nature Communications, 6, Article number: 7316, 2015, [DOI], PMC4557300
  320. Lemkul, J.A., Roux, B., van der Spoel, D and MacKerell, A.D., Jr., "Implementation of Extended Lagrangian Dynamics in GROMACS for Polarizable Simulations Using the Classical Drude Oscillator Model," Journal of Computational Chemistry, 36: 1480-1486, 2015, [DOI], PMC4481176
  321. Yang, M., Huang, J., and MacKerell, A.D., Jr., "Enhanced Conformational Sampling Using Replica Exchange with Concurrent Solute Scaling and Hamiltonian Biasing Realized in One Dimension," Journal of Chemical Theory and Computation, 11: 2855-2867, 2015, [DOI], PMC4463548
  322. Jana, M. and MacKerell, A.D., Jr., "CHARMM Drude Polarizable Force Field for Aldopentofuranoses and Methyl-aldopentofuranosides," Journal of Physical Chemistry B, 119: 7846-7859, 2015, [DOI], PMC4483154
  323. Yang, W., Sun, X., Yu, W., Rai, R., Deschamps, J., Mitchell, L., Jiang, C., MacKerell, A.D., Jr., Xue, F., "Facile Synthesis of Spirocyclic Lactams from alpha-keto Carboxylic Acids." Organic Letters, 17: 3070-3073, 2015, [DOI]
  324. Chen, W., Shi, C., MacKerell, A.D., Jr. and Shen, J. "Conformational Dynamics of Two Natively Unfolded Fragment Peptides: Comparison of the AMBER and CHARMM Force Fields," The Journal of Physical Chemistry B, 119: 7902-7910, 2015, [DOI], PMC4685472
  325. Passaniti, A., Brusgard, J., Choe, M., Chumsri, S., Renoud, K., MacKerell, A.D., Jr, and Sudol, M., "RUNX2 and TAZ-dependent signaling pathways regulate soluble E-Cadherin levels and tumorsphere formation in breast cancer cells," Oncotarget, 6: 28132-28150. 2015, [DOI]
  326. Domene, C., Jorgensen, C., Vanommeslaeghe, K., Schofield, C., MacKerell, A.D., Jr., "Quantifying the binding interaction between the hypoxia-inducible transcription factor and the von Hippel Lindau suppressor," Journal of Chemical Theory and Computation, 11: 3946-3954, 2015, [DOI]
  327. Savelyev, A., and MacKerell, A.D., Jr. "Differential Deformability of the DNA Minor Groove and Altered BI/BII Backbone Conformational Equilibrium by the Monovalent Ions Li+, Na+, K+ and Rb+ via Water-Mediated Hydrogen Bonding," Journal of Chemical Theory and Computation, 11: 4473-4485, 2015, [DOI], PMC4654687
  328. Drennen, B., MacKerell, A.D., Jr. and Fletcher, S. "Expedient access to alpha-helix mimetics based on an isocinchomeronic acid core," Tetrahedron Letters, 56, 6819-6822, [DOI],
  329. Lee, J., Cheng, X., Swails, J., Yeom, M.Sun.,Eastman, P., Lemkul, J., Wei, S., Buckner, J., Jeong, J.Ch., Qi, Y., Jo, S., Pande, V., Case, D., Brooks, C., MacKerell, A, Klauda, J., and Im, W., "CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations using the CHARMM36 Additive Force Field," Journal of Chemical Theory and Computation, 12: 405-413, 2015, PMC4712441, [DOI]
  330. Lakkaraju, S.K., Lemkul, J.A., Huang, J., and MacKerell, A.D., Jr. "DIRECT-ID: An Automated Method to Identify and Quantify Conformational Variations - Application to β2-adrenergic GPCR," Journal of Computational Chemistry, 37: 416–425, 2015, PMC4756637, [DOI]
  331. 2016

  332. Lemkul, J.A., Huang, J. and MacKerell, A.D., Jr. "Induced Dipole-Dipole Interactions Influence the Unfolding Pathways of Wild-Type and Mutant Amyloid β-Peptides," Journal of Physical Chemistry B, 119: 15574-15582, 2015, PMC4690986, [DOI]
  333. Xu, Y., Vanommeslaeghe, K., Aleksandrov, A., MacKerell, A.D., Jr. Nilsson, L., "Additive CHARMM force field for naturally occurring modified ribonucleotides," Journal of Computational Chemistry, In Press, 2016, [DOI]
  334. Lemkul, J.A., Huang, J., Roux, B., and MacKerell, A.D., Jr. "An Empirical Polarizable Force Field Based on the Classical Drude Oscillator Model: Development History and Recent Applications," Chemical Reviews, 116: 4983–5013, 2016, [DOI]
  335. Lanning, M.E., Yu,W., Yap, J.l., Chauhan, J., Chen, L., Whiting, E., Pidugu, L.S., Atkinson, T, Bailey, H., Li, W., Roth, B.M., Hynicka,L., Chesko, K., Toth, E.A., Shapiro, P., MacKerell, Jr, A.D., Wilder, P.T. and Fletcher, F., "Structure-Based Design of N-Substituted 1-Hydroxy-4-sulfamoyl-2-naphthoates as Selective Inhibitors of the Mcl-1 Oncoprotein," European Journal of Medicinal Chemistry," 113: 272-292, 2016, [DOI]
  336. Cavalier, M.C., Ansari, M.I., Pierce, A.D., Wilder, P.T., McKnight, L.E., Raman, E.P., Neau, D.B., Bezawada, P., Alasady, M.J., Varney, K.M., Toth, E.A., MacKerell Jr., A.D., Coop, A., Weber, D.J., "Small Molecule Inhibitors of Ca2+-S100B Reveal Two Protein Conformations," Journal of Medicinal Chemistry, 59: 592-608, 2016, PMC4732916, [DOI]
  337. Glassford, I., Teija, C.N., Daher, S.S., Weil, A., Small, M.C., Redhu, S.K., Colussi, D.J., Jacobson, M.A., Childers, W., Buttaro, B., Nicholson, A.W., MacKerell, A.D., Jr., Cooperman, B.S., Andrade, R.B. "Ribosome-templated azide−alkyne cycloadditions: synthesis of potent macrolide antibiotics by in situ click chemistry," Journal of the American Chemical Society, 138: 3136-3144, 2016, PMC4785600, [DOI]
  338. Cavalier, M.C., Melville, Z., Aligholizadeh, E., Raman, E.P., Yu, W., Fang, L., Alasady, M., Pierce, A.D., Wilder, P.T., MacKerell, A.D., Jr. and Weber, D.J. "Novel protein-inhibitor interactions in site 3 of Ca2+-bound S100B as discovered by X-ray crystallography," Acta Crystallographica Section D, D72, 753-760, 2016, [DOI]
  339. Astudillo, L, da Silva, T.G., Wang, Z., Han, X., Jin, K., VanWye, J., Zhu, X., Weaver, K.L,, Oashi, T., Lopes, P.E.M., Orton, D., Neitzel, L.R., Lee, E., Landgraf, R., Robbins, D.J., MacKerell, A.D., Jr. and Capobianco, A.J. "Inhibitor of Mastermind Recruitment (IMR-1): A Small Molecule Inhibitor of the Notch Transcriptional Activation Complex," Cancer Research, 76:3593-3603, 2016, PMC4911243, [DOI]
  340. Feng, Y., Huang, J., Kim, S., Shim, J.-H., MacKerell, A.D., Jr., and Ge, N.-H. "Structure of Penta-Alanine Investigated by Two-Dimensional Infrared Spectroscopy and Molecular Dynamics Simulation," Journal of Physical Chemistry B, 120:5325-5339, 2016, [DOI]
  341. Cardenas, M.G., Yu, W.,* Beguelin, W., Teater, M., Geng, H., Goldstein, R., Oswald, E., Hatzi, K., Yang, S.-N., Cohen, J., Shaknovich, R., Vannomeslaeghe, K., Cheng, H., Liang, D., Cho, H.J., Abbott, J., Cerchietti, L, Cierpicki, T., Xue, F., MacKerell, A.D., Jr., and Melnick, A.M., "Therapeutic targeting of GCB- and ABC-DLBCLs by rationally designed BCL6 inhibitors," Journal of Clinical Investigation, In Press, 2016, [DOI]
  342. Xu, Y., MacKerell, A.D., Jr., and Nilsson, L. "Structural effects of modified ribonucleotides and magnesium in transfer RNAs," Bioorganic & Medicinal Chemistry, In Press, 2016, [DOI]
  343. Soteras Gutiérrez, I., Lin, F.-Y., Vanommeslaeghe, K., Lemkul, J.A., Armacost, K.A., Brooks, Cl., III, and MacKerell, A.D., Jr., "Parametrization of Halogen Bonds in the CHARMM General Force Field: Improved treatment of ligand-protein interactions," Bioorganic & Medicinal Chemistry, In Press, 2016, [DOI]
  344. Yang, M., Angles d’Ortoli, T., Säwén, E., Jana, M., Widmalm, G., and MacKerell, A.D., Jr.,"Delineating the conformational flexibility of trisaccharides from NMR spectroscopy experiments and computer simulations," Physical Chemistry Chemical Physics, 18: 18776-18794, 2016, A, PMC494544, [DOI]
  345. Heinzl, G., Huang, W,. Yu, W, Giardina, B., Zhou, Y, MacKerell, A.D., Jr. Wilks, A., and Xue, F., "Benzimidoguanidines as Allosteric Inhibitors of the Iron-Regulated Heme Oxygenase (HemO) of Pseudomonas aeruginosa," Journal of Medicinal Chemistry, 2016, 59:6929-6942, 2016, [DOI]
  346. Sarkar, A., Yu, W., Desai, U.R., MacKerell, A.D., Jr., and Mosier, P. "Estimating glycosaminoglycan–protein interaction affinity: Water dominates the specific antithrombin–heparin Interaction," Glycobiology, 26: 1041-1047, 2016, [DOI]
  347. Chauhan, J., Cardinale, S., Fang, L., Huang, J., Kwasny, S.M., MacKerell, A.D., Jr., Opperman, T.J., Fletcher, S., and Erik P.H. de Leeuw, E.P.H. "Towards Development of Small Molecule Lipid II inhibitors as Novel Antibiotics," PLoS ONE, 11: e0164515, 2016, PMC5077133 [DOI]
  348. Khan, H.M., Grauffel, C., Broer, R., MacKerell, A.D., Jr., Havenith, R.W.A., and Reuter, N., "Improving the force field description of tyrosine-choline cation-π interactions: QM investigation of phenol-N(Me)4+ interactions," Journal of Chemical Theory and Computation, 12: 5585-5595, 2016, NIHMSID823369 [DOI]
  349. Huang, J., Rauscher, S., Nawrocki, G., Ran, T., Feig, M, de Groot, B.L., Grubmüller, H., and MacKerell, A.D., Jr., "CHARMM36m: An Improved Force Field for Folded and Intrinsically Disordered Proteins," Nature Methods, 14:71-73, 2016, PMC5199616,[DOI]
  350. Lemkul, J.A., Lakkaraju, S.K., and MacKerell, A.D., Jr., "Characterization of Mg2+ Distributions around RNA in Solution, ACS Omega, 1:680-688, 2016, PMC5088455 [DOI]
  351. Raman, E.P., Lakkaraju, S.K., Denny, R.A., and MacKerell, A.D., Jr. "Estimation of relative free energies of binding using pre-computed ensembles based on the single-step free energy perturbation and the site-identification by ligand competitive saturation approaches," Journal of Computational Chemistry, In Press, 2016, NIHMSID823276 [DOI]
  352. Jo, S., Cheng, X., Lee, J., Kim, S., Park, S.-J., Patel, D.S., Beaven, A.H., Lee, K.I., Rui, H., Roux, B., MacKerell, A.D., Jr., Klauda, J.B., Qi, Y., and Im, W. "CHARMM-GUI 10 Years for Biomolecular Modeling and Simulation," Journal of Computational Chemistry, In Press, 2016, PMID 27862047, [DOI]
  353. Lemkul, J.A. and MacKerell, A.D., Jr., "Balancing the Interactions of Mg2+ in Aqueous Solution and with Nucleic Acid Moieties For a Polarizable Force Field Based on the Classical Drude Oscillator Model," Journal of Physical Chemistry B, 120: 11436–11448, 2016, PMC5148688 [DOI]
  354. Huang, J., Lakkaraju, S.K., Coop, A. and MacKerell, A.D., Jr. "Conformational Heterogeneity of Intracellular Loop 3 of the µ-Opioid G-Protein Coupled Receptor," Journal of Physical Chemistry B, 120: 11897–11904, 2016, PMC5148698 [DOI]
  355. Cardenas, M.G., Oswald, E., Yu, W. Xue, F., MacKerell, A.D., Jr. and Melnick, "The expanding role of the BCL6 oncoprotein as a cancer therapeutic target," Clinical Cancer Research, In press, 2016, PMID 27881582, [DOI]
  356. Yang, M., Simon, R., and MacKerell, A.D., Jr. "Conformational Preference of Serogroup B Salmonella O Polysaccharide in Presence and Absence of the Monoclonal Antibody Se155-4: Implications for Vaccine Design," Journal of Physical Chemistry B, In press, 2016, NIHMSID 831796. [DOI]
  357. Small, M.C., Aytenfisu, A.H., Lin, F.-Y. He, X., and MacKerell, A.D., Jr., "Drude Polarizable Force Field for Aliphatic Ketones and Aldehydes, and their Associated Acyclic Carbohydrates," Journal of Computer-Aided Molecular Design, In Press, 2017, 10.1007/s10822-017-0010-0 [DOI]
  358. 2017

  359. Huang, J., Mei, Y., Konig, G., Simmonett, A.C., Pickard, F.C., Wu, Q., Wang, L.-P., MacKerell, A.D., Jr., Brooks, B.R., and Shao, Y., "An Estimation of Hybrid Quantum Mechanical Molecular Mechanical (QM/MM) Polarization Energies for Small Molecules Using Polarizable Force-Field Approaches," Journal of Chemical Theory and Computation, In Press, 2017, , NIHMSID 843716 [DOI]


Book Chapters

  1. Pietruszko, R. Ferencz-Biro, K. and MacKerell, Jr. A.D. "Chemical modification of human aldehyde dehydrogenase," In Enzymology of Carbonyl Metabolism 2, H. Weiner and T.G. Flynn Eds. Alan R. Liss Inc. New York, pp. 29-41, 1985.
  2. Pietruszko, R. MacKerell, Jr. A.D. and Ferencz-Biro, K. "Adducts of propionaldehyde and 3,4-dihydroxyphenylacetaldehyde with human liver aldehyde dehydrogenase," In Aldehyde Adducts in Alcoholism M.A. Collins Ed. Alan R. Liss Inc. New York, pp. 67-74, 1985.
  3. MacKerell, Jr. A.D. Rigler, R. Hahn, U. and Saenger, W. "Ribonuclease T1: Interaction with 2'GMP and 3'GMP as studied by time resolved fluorescence spectroscopy," In Structure, Dynamics and Function of Biomolecules A. Ehrenberg, R. Rigler, A. Graslund and L. Nilsson Eds. Springer Series in Biophysics, Vol. 1. Springer-Verlag, pp. 260-264, 1987.
  4. Pietruszko, R. and MacKerell, Jr. A.D. "Stoichiometry of chemical modification of human aldehyde dehydrogenase: Evidence for 'Quarter of the sites' reactivity," In Enzymology and Molecular Biology of Carbonyl Metabolism: Aldehyde Dehydrogenase, Aldo-Keto Reductase and Alcohol Dehydrogenase H. Weiner Ed. Progress in Clinical and Biological Research, Vol.232, Alan R. Liss Inc. New York, pp. 37-52. 1987.
  5. Rigler, R. MacKerell, Jr. A. D. Vogel, H. and Nilsson, L. "Picosecond spectroscopy of molecular dynamics of proteins and enzymes," In Laser Spectroscopy VIII (EICOLS 87) W. Persson and S. Svanberg Eds. pp. 242-244, 1988.
  6. Schlenkrich, M. Brickmann, J. MacKerell, Jr. A.D. and Karplus, M. "An Empirical Potential Energy Function for Phospholipids: Criteria for Parameter Optimization and Applications," In Biological Membranes: A Molecular Perspective from Computation and Experiment K.M. Merz, Jr. and B. Roux, Eds. Birkhäuser, Boston, 1996.
  7. MacKerell, Jr. A.D. "Observations on the A versus B equilibrium in molecular dynamics simulations of duplex DNA and RNA," ACS Symposium Series, "Molecular Modeling and Structural Determination of Nucleic Acids," N.B. Leontis, Ed. pp. 304-311, 1997.
  8. MacKerell, Jr. A.D. "Protein Force Fields," In Encyclopedia of Computational Chemistry P.v.R. Schleyer, N.L. Allinger, T. Clark, J. Gasteiger, P.A. Kollman, H.F. Schaefer III, P.R. Schreiner, Eds. John Wiley & Sons, Chichester, 1998.
  9. MacKerell, Jr. A.D. Brooks, B. Brooks, III, C.B. Nilsson, L. Roux, B. Won, Y. and Karplus, M. "CHARMM: The Energy Function and Its Parametrization with an Overview of the Program," In Encyclopedia of Computational Chemistry P.v.R. Schleyer, N.L. Allinger, T. Clark, J. Gasteiger, P.A. Kollman, H.F. Schaefer III, P.R. Schreiner, Eds. John Wiley & Sons, Chichester, Vol. 1, 271-277, 1998.
  10. MacKerell, Jr. A.D. "Atomistic Models and Force Fields," In Computational Biochemistry and Biophysics O. Becker, A.D. MacKerell, Jr. B. Roux and M. Watanabe, Eds. Marcel Dekker Inc. New York, 7-38, 2001.
  11. MacKerell, Jr. A.D. Nilsson, L. "Nucleic Acid Simulations," In Computational Biochemistry and Biophysics O. Becker, A.D. MacKerell, Jr. B. Roux and M. Watanabe, Eds. Marcel Dekker Inc. New York, 441-463, 2001.
  12. MacKerell, Jr. A.D. "Interatomic Potentials: Molecules," In Handbook of Materials Modeling S. Yip, Ed. Lancaster Publishing Services, Lancaster, UK, 2005.
  13. MacKerell, Jr. A.D. "Empirical Force Fields," In Computational Methods for Protein Structure Prediction and Modeling I: Basic Characterization Y. Xu, D. Xu, J. Liang, Eds. Springer, New York, pp. 45-69, 2007.
  14. MacKerell, Jr. A.D. and Nilsson, L. "Theoretical Studies of Nucleic Acids and Nucleic Acid-Protein Complexes using CHARMM," In Computational Studies of RNA and DNA J. Sponer and F. Lankas, Eds. Springer, Netherlands, pp. 73-94, 2006.
  15. Guvench, O. and MacKerell, Jr. A.D. "Comparison of protein force fields for molecular dynamics simulations," In Molecular Modeling of Proteins, A. Kukol, Ed. Humana Press, Humana Press. 2008 (Methods Mol Biol. 2008;443:63-88. PMID: 18446282)
  16. Klauda, J.B., Venable, R.M., MacKerell, A.D., Jr. and Pastor, R.W. "Considerations for Lipid Force Field Development," In Computational Modeling of Membrane Bilayers, S. Feller, Editor, Elsevier, Inc. Chapter 1, pp 1-48, 2008.
  17. Priyakumar, U.D. and MacKerell, A.D., Jr., "Molecular Modeling of Base Flipping in DNA, "In DNA and RNA modification Enzymes : Comparative Structure, Mechanism, Functions, Cellular Interactions and Evolution," Henri Grosjean, Editor, LANDES Biosciences Intelligence Unit, 2009
  18. Lopes, P.E.M, Harder, E., Roux, B., and MacKerell, A.D., Jr. "Formalisms for the explicit inclusion of electronic polarizability in molecular modeling and dynamics studies," in "Multi-scale Quantum Models for Biocatalysis: Modern Techniques and Applications" Volume editors Darrin York and Tai-Sung Lee; in the series, Challenges and Advances in Computational Chemistry and Physics, Vol. 7, Editor J. Leszczynski, p 219-218, 2009, ISBN: 978-1-4020-9955-7
  19. Baker, C.M., Darian, E. and MacKerell, A.D., Jr. "Towards Biomolecular Simulations with Explicit Inclusion of Polarizability: Development of a CHARMM Polarizable Force Field based on the Classical Drude Oscillator Model," Innovations in Biomolecular Modeling and Simulations, 2012, pp. 23-50,[DOI]
  20. Zhong, S., Oashi, T., Yu, W., Shapiro, P., and MacKerell, A.D., Jr. "Prospects of modulating protein-protein interactions," In Protein-Ligand Interactions H. Gohlke ED., Methods and Principles in Medicinal Chemistry, Wiley-VCH Verlag Gmbh & Co. KGaA, Weinheim, Germany, p 295-329, 2012, ISBN: 978-3-527-32966-3
  21. Hartman, K.G., Wilder, W.T., Varney, K., MacKerell, A.D., Jr., Coop, A., Njar, V., Zimmer, D., Lapidus, R., and Weber, D.J, "Inhibiting S100B in Malignant Melanoma," in "Melanoma - From Early Detection to Treatment," G. Huynh and T. Duc, editors, INTECH Open Science, Chapter 24, 2013, [DOI]
  22. Yu, W., Guvench, O., and MacKerell, A.D., Jr., "Computational approaches for the design of PPI inhibitors," in "Understanding and exploiting protein—protein interactions as drug targets," e-book, Future Science Limited, pp. 90-102, 2013, [DOI]
  23. Mallajosyula, S.S., Jo, S., Im, W., and MacKerell, A.D., Jr., "Molecular Dynamics Simulations of Glycoproteins using CHARMM," Methods in Molecular Biology: Glycoinformatics. Chapter 25, Humana Press, New York, NY, 2014, PMC4537648, [DOI]
  24. Savelyev, A., Roux, B., and MacKerell, A.D., Jr., "Explicit Inclusion of Induced Polarization in Atomistic Force Fields Based on the Classical Drude Oscillator Model," in "Many-Body Effects and Electrostatics in Biomolecules," Q. Cui and M. Meuwley, Editors, Pan Stanford Publishing, In Press, 2014
  25. Lopes, P.E.M., Guvench, O., and MacKerell, A.D., Jr., Current Status of Protein Force Fields for Molecular Dynamics, In Molecular Modeling of Proteins, 2nd edition, A. Kukol, Editor, Humana Press. Chapter 3, pp. 47 -72, 2014, [DOI], (Methods in Molecular Biology, 1215: 47-72, 2014).
  26. Jo, S., Cheng, X., Islam, S.M., Huang, L., Rui, H., Zhu, A., Lee, H.S., Qi, Y., Han, W., Vanommeslaeghe, K., MacKerell, A.D., Jr., Roux, B., and Im, W. "CHARMM-GUI PDB Manipulator for Advanced Modeling and Simulations of Proteins Containing Nonstandard Residues," in Advances in Protein Chemistry and Structural Biology: Biomolecular Modelling and Simulations, T. Karabencheva-Christova, Editor, Elsevier, New York, Chapter 8, 235-266, 2014, [DOI]
  27. Faller, C.E., Prabhu Raman, E.P., MacKerell, A.D., Jr. and Guvench, O. "Site Identification by Ligand Competitive Saturation (SILCS) Simulations for Fragment-Based Drug Design," in Fragment-Based Methods in Drug Discovery, Chapter 7, Anthony E. Klon (ed.), (Methods in Molecular Biology, vol. 1289, Springer Science+Business Media, New York, 2015, ISBN 978-1-4939-2485-1 [DOI]
  28. Small, M.C., and MacKerell, A.D., Jr., "Force field representation of biomolecular systems," in in Silico Drug Discovery and Design: Theory, Methods, Challenges and Applications, Chapter 2, CRC Press: Taylor & Francis Group, ISBN (978-1-4822-1783-4)