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Mackerell.umaryland.edu

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. 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
3. MacKerell, Jr., A.D., McWright, R.S. and Pietruszko, R., Bromoacetophenone as an affinity reagent for human aldehyde dehydrogenase. Biochemistry 25:5182-5189, 1986
4. MacKerell, Jr., A.D., and Pietruszko, R., Chemical modification of human aldehyde dehydrogenase by substrate., Biophysica Biochemica Acta 911:306-317, 1986
5. 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
6. 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
7. 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
8. MacKerell, Jr., A.D., Molecular modeling and dynamics of neuropeptide Y. Journal of
Computer-Aided Molecular Design 2:55-63, 1988
9. 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
10. 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 pharmacological activity measurements., Regulatory Peptides 25:295-313, 1989
11. 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
12. 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.
13. 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.
14. 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.
15. 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.
16. 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.
17. 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.
18. 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.
19. 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
20. 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.
21. 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.
22. 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.
23. 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.
24. 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.
25. 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,
26. 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.
27. 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.
28. 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.
29. 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.
30. 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.
31. 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.
32. 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.
33. 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.
34. Lieske, S., Yang, B., Eldefrawi, M.E. and MacKerell Jr., A.D., and Wright, J., (-)3β- Substituted Ecgonine Methyl Esters as Inhibitors for Cocaine Binding and Dopamine
Uptake., Journal of Medicinal Chemistry, 41: 864-876, 1998.
35. 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.
36. 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.
37. Uvdal, P., Åsmundsson, R. and MacKerell, A.D., Jr., Experimental vibrational shifts induced by 13C isotopic substitution assigned by ab initio calculations., Physical Review Letters, 82:
125-128, 1999.
38. Pastor, N., MacKerell, A.D., Jr., 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.
39. 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,
40. 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.
41. 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.
42. 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
, 2000, 103: 483-494.
43. 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.
44. 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.
45. 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.
46. Barsky, D., Foloppe, N., Ahmadia, S., Wilson, III, D.M., MacKerell, Jr., A.D., New Insights into the Structure of Abasic DNA from Molecular Dynamics Simulations., Nucleic Acids
Research
, 28: 2613-2626, 2000.
47. 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.
48. 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.
49. 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.
50. 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.
51. Marquez, V.E., Wang, P., Nicklaus, M.C., Maier, M., Manoharan, M., Christman, J.K., Banavali, N.K., and MacKerell, A.D., Jr., Inhibtion 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.
52. 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.
53. 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.
54. 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.
55. 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.
56. 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.
57. 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.
58. 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.
59. 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.
60. 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.
61. 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.
62. 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.
63. Pan, Y., Huang, N., Cho, S. and A. D. MacKerell, Jr., “Consideration of molecular weight during compound selection in virtual database screening,” Journal of Chemical
Information and Computer Science
, 43: 267-272, 2003.
64. 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, PMID: 12506195.
65. 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.
66. 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.
67. 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.
68. Lamoureux, G., MacKerell, A.D., Jr., Roux, B., A simple polarizable model of water based on classical Drude oscillators, Journal of Chemical Physics, 119: 5185-5197, 2003
69. Pan, Y. and MacKerell, A.D., Jr., Altered structural fluctuations in duplex RNA versus DNA: A conformational switch involving base pair opening. Nucleic Acids Research, 31: 7131-
70. Huang, N. and MacKerell, A.D., Jr., Atomistic view of base flipping in DNA. Philosophical
Transactions of The Royal Society, London, A, 362: 1439-1460, 2004
71. MacKerell, A.D., Jr., 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.
72. Rosen, G.M, Beselman, A., Tsai, P., Pou, S., Mailer, C. Ichikawa, K,. Robinson, B.H., Nielsen, R., Halpern, H. and MacKerell, A.D. Jr., 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.
73. Macias, A., Hernandez, R.J., Mehta, A.K., MacKerell, A.D., Jr., 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.
74. Huang, N., Nagarsekar, A., Xia, G., Hayashi, J., MacKerell, A.D., Jr., 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
75. MacKerell, A.D., Jr,. Feig, M., Brooks, C.L., III, 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.
76. Patel, S., MacKerell, A.D., Jr., Brooks, C.L., III, 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
77. MacKerell, A.D., Jr., Empirical Force Fields for Biological Macromolecules: Overview and Issues, Journal of Computational Chemistry, 25: 1584-1604, 2004
78. Horton, J.R., Ratner, G., Banavali, N.K., Huang, H,. Choi, Y., Maier, M.A., Marquez, V.E., MacKerell, A.D., Jr, 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. PMID: 15273274
79. Mason, P. E., Neilson, G. W., Enderby, J. E., Saboungi, M.-L., Dempsey, C. E.; MacKerell, A. D., Jr., Brady, J. W. “The Structure of Aqueous Guanidinium Chloride Solutions,”
Journal of the American Chemical Society, 126; 11462-11470, 2004, DOI:
10.1021/ja040034x
80. Markowitz, J., Chen, I., Gitti, R., Baldisseri, D. M., Pan, Y., Udan, R., Carrier, F., MacKerell, A. D., Jr., 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.
81. Wymore, T. ,Hempel, J., Cho, S.C., MacKerell, A.D., Jr., Nicholas, H.B. Jr., Deerfield, D.W., II, “Molecular recognition of aldehydes by aldehyde dehydrogenase and mechanism of nucleophile activation, Proteins: Structure, Function, and Bioinformatics, 57: 758-777,
2004
82. Pitman, M.C., Frank Suits, F., MacKerell, A.D., Jr., Feller, S.E., “Molecular Level Organization of Saturated and Polyunsaturated Fatty Acids in a Phosphatidylcholine Bilayer Containing Cholesterol, Biochemistry, 43:15318-15328, 2004
83. Huang, N, MacKerell, A.D., Jr., “Specificity in Protein-DNA Interactions: Energetic Recognition by the (Cytosine-C5)-methyltransferase from HhaI.” Journal of Molecular
Biology. 345: 265-274, 2005
84. Wu, H., D. Bernard, W. Chen, G.D. Strahan, J.R. Deschamps, D.A. Parrish, J.W. Lewis, A.D. MacKerell, Jr., and A. Coop, “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
85. Klauda, J.B., Brooks, B.R., MacKerell, A.D., Jr., 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, PMID: 16863197
86. MacKerell, A.D., Jr., “Empirical Force Fields for Proteins: Current Status and Future Directions, “ Annual Reports in Computational Chemistry, 1: 91-102, 2005
87. Anisimov, V.M., Lamoureux, G., Vorobyov, I.V., Huang, N., Roux, B. and MacKerell, A.D., Jr. “Determination of Electrostatic Parameters for a Polarizable Force Field Based on the
Classical Drude Oscillator,” Journal of Chemical Theory and Computing,” 1: 153-168,
2005.
88. Pan, Y., Priyakumar, D. and MacKerell, A.D., Jr., “Conformational Determinants of Tandem GU Mismatches in RNA: Insights from molecular dynamics simulations and quantum mechanical calculations,” Biochemistry, 44: 1433-1443, 2005.
89. Boresch, S., Leitgeb, M., Beselman, A., MacKerell, A.D., Jr., “Unexpected relative aqueous solubilities of a phosphotyrosine analogue and two phosphonate derivatives” Journal of the
American Chemical Society
, 127; 4640-4648, 2005
90. H. Wu, L. N. Thatcher, D. Bernard, D. A. Parrish, J. R. Deschamps, K. C. Rice, A. D. MacKerell Jr., A. Coop: 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
91. Bernard, D., Coop, A. and MacKerell, Jr., A.D. “Computer-Aided Drug Design: Structure- Activity Relationships of Delta Opioid Ligands.” Drug Design Reviews, 2005, 2: 277-291.
92. 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, 2005, 48; 4586-4595.
93. 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
, 2005, 26: 1452-1463.
94. 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, PMCID: PMC1180745.
http://nar.oxfordjournals.org/cgi/reprint/33/13/4212?ijkey=UTMV7oMutgQrEd2&keytype=ref 95. 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.
96. 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 Computing, 2006,
2:187-200.
97. Markowitz, J., MacKerell, A. D., Jr., Carrier, F., Charpentier, T.H., Weber, D. J. Design of Inhibitors of S100B,” Current Topics in Medicinal Chemistry, 2005, 5: 1093-1108.
98. Bernard, D.; Coop, A.; MacKerell, A. D., Jr., “Conformationally Sampled Pharmacophore for Peptidic δ Opioid Ligands,: Journal of Medicinal Chemistry, 48: 7773-7780, 2005, PMCID:
99. 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 p56lck,” Journal of Chemical Information and
Modeling, 45: 1759-1766, 2005.
100. Buck, M., Bonnet, S., Pastor, R.W. and MacKerell, Jr., A.D. “Importanceof the CMAP correction to the CHARMM22 Protein Force Field: dynamics of hen lysozyme" Biophysical
Journal, 2006, 90: L36-L38, On line: Dec. 16, 2005, doi:10.1529/biophysj.105.078154,
101. 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, 2006, 418: 245-249.
102. Priyakumar , U.D. and 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), 2006, 128:678-679, PMCID:
103. 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, 2006, 2, 213-222.
104. Priyakumar, U.D. and MacKerell, Jr., A.D. “Computational Approaches for Investigating Base Flipping in Oligonucleotides,” Chemical Reviews, 2006, 106: 489-505.
105. 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, 2006, 110: 10997-11004,
106. 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, DOI: 10.1021/jp0623241, PMID: 16898697 107. Mayaan, E., Moser, A., MacKerell, Jr., A.D., 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, NIHMSID # 197800
108. 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,
PMCID: PMC2526287
109. 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.
110. Lopes, P.E.M., Murashov, V. Tazi, M. Demchuk, E. MacKerell, A. D., Jr. “Development of an Empirical Force Field for Silica. Application to the Quartz-Water Interface,” Journal of Physical
Chemistry B, 110: 2782-2792, 2006, PMCID: PMC2531191
111. Zhong, S., Macias, A.T., MacKerell, Jr., A.D. “Computational identification of the inhibitors of protein-protein interactions,” Current Topics in Medicinal Chemistry, 7, 63-
112. Chen, F., Hancock, C.N., Macias, A.T., Joh, J., Still, K., Zhong, S., MacKerell, Jr., A.D. 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, PMCID: PMC1857279
113. Almond, A. Blundell, C., Higman, V., MacKerell, Jr., A.D., 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,
114. 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, PMID: 17584159.
115. Vorobyov, I.V., Anisimov, V.M., Greene, S., Venable, R.M., Moser, A., Pastor, R.W. and MacKerell, A.D., Jr., Additive and Classical Drude Polarizable Force Fields for Linear and Cyclic Ethers, Journal of Chemical Theory and Computation, 3: 1120-1133, 2007. DOI:
116. Lopes, P., Lamoureux, G., Roux, B., MacKerell, Jr., A.D., Journal of Physical
Chemistry B, 111:2873-2885, 2007. PMC2519011
117. Macias, A.T., Banavali, N.K. and MacKerell, Jr. A.D. “DNA bending induced by carbocyclic sugar analogs constrained to the north conformation,” Biopolymers, 85:438-449,
118. Woodcock, H.L., Moran, D., Pastor, R.W., MacKerell, Jr., A.D., 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, PMCID: PMC1914444
119. Guvench, O., Qu, C.K., MacKerell, A.D., Jr., “Tyr66 acts as a conformational switch in the closed-to-open transition of the SHP-2 N-SH2-domain phosphotyrosine-peptide binding cleft” BioMed Centeral (BMC) Structural Biology 7:14, 2007, PMCID: PMC1847519
120. Bernard, D., Coop, A. and MacKerell, Jr., A.D. “Quantitative Conformationally Sampled Pharmacophore for delta Opioid Ligands: Reevaluation of Hydrophobic Moieties Essential for Biological Activity,” Journal of Medicinal Chemistry, 50: 1799-1809, 2007.
121. Furci, L.M., Lopes, P., Eakanunkul, S., Zhong, S., MacKerell, A.D., Jr., 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.
122. 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, PMCID: PMC2542883
123. 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;
124. Xie, W., Pu, J, MacKerell, Jr., A.D., 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. PMCID: PMC2572772
125. Thomas, J.L., Tobias, D.J., 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 (Letter), 111:12941-12944, 2007, PMCID:
126. Li, L., Vorobyov, I.V., MacKerell, Jr., A.D., Allen, T.W., “Is arginine charged in a membrane?” Biophysical Journal, 94: L11-L13, 2008, PMCID: PMC2157258
127. Priyakumar, U.D., 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, NIHMSID 197573
128. Guvench, O. and MacKerell, Jr., A.D., “Automated conformational energy fitting for force- field development,” Journal of Molecular Modeling, 14, 667-679, 2008, DOI
10.1007/s00894-008-0305-0, NIHMSID 196768 129. Chen, X., Zhong S., Zhu, X., Dziegielewska, B., Ellenberger, T., Wilson, G.M, Bachman, K., 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-
130. Harder, E., Anisimov, V.M., Whitfield, T., MacKerell, Jr., A.D., 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
131. MacKerell, Jr., A.D., Nilsson, L., “Molecular dynamics simulations of nucleic acid-protein complexes,” Current Opinions in Structural Biology, 18: 194-199, 2008,
132, Lopes, P.E.M., Demchuk, E., 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.
133. Guvench, O., Greene, S.N., Kamath, G., Brady, J.W., Venable, R.M., Pastor, R.W., MacKerell, Jr., A.D. “Additive empirical force field for hexopyranose monosaccharides” Journal of Computational Chemistry, 29: 2543-2564, 2008. NIHMSID 196771
134. Lee, H., Venable, R.M., MacKerell, Jr. A.D., Pastor, R.W. “Molecular dynamics studies of polyethylene oxide and polyethylene glycol: Hydrodynamic radius and shape anisotropy,” Biophysical Journal, 95: 1590-1599, 2008, DOI 10.1529/biophysj.108.133025, PMCID:
135. 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:
136. MacKerell, Jr., A.D., Shim, J.-H., 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, DOI: 10.1021/ct8000969,
137. 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.
138. Acharya, C., Seo, P.R., Polli, J.E. 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, DOI: 10.1021/mp800035h, PMID: 18710255
139. 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, PMC2788817
140. Lopes, P.E.M., Lamoureux, G., 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, PMC251901
141. Charpentier, T.H., Wilder, P.T., Liriano, M.A., Varney, K.M., Pozharski, E, MacKerell, Jr., A.D., Coop, A., Toth, E.A., Weber, D.J., “Divalent metal ion complexes of S100B in the absence and presence of pentamidine,” Journal of Molecular Biology, 382:56-73, 2008,
142. 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. PMC2784611
143. 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,
144. 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:
145. 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
146. Guvench, O., and MacKerell, Jr., A.D. “Computational evaluation of protein – small molecule binding,” Current Opinion in Structural Biology, 19:56–61, 2009. PMC2671234
147. 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-
148. 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.
149. Banavali, N. and MacKerell, Jr., A.D., “Characterizing structural transitions using localized free energy landscape analysis, “ PLOS One, 4: e5525, 2009, doi:10.1371 / 150. 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, PMC2760998
151. 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., Karplus, M. “CHARMM: The biomolecular simulation program,” Journal of Computational Chemistry, 30: 1555-
152. Guvench, O., and MacKerell, Jr., A.D. “Computational Fragment-Based Binding Site Identification by Ligand Competitive Saturation, PLoS Computational Biology, 5:
154. 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., 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,
155. Sorci, L., Pan,, Y., Eyobo, Y. Rodionova, I., Huang, N. Kurnasov, O., Zhong, S., MacKerell, Jr., A.D., Zhang, H., Osterman, A.L., "Targeting NAD biosynthesis in bacterial pathogens. Structure-based development of inhibitors of nicotinate mononucleotide adenylyltransferase
NadD" Chemistry and Biology, 16:849-61, 2009, PMC2770502.
156. 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, NIHMSID197600, PMC2888514
157. 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, PMC2741538
158. Guvench, O., Hatcher, E. R., Venable, R. M., Pastor, R. W., MacKerell, A. D. Jr. “Additive Empirical CHARMM Force Field for glycosyl linked hexopyranoses,” Journal of Chemical
Theory and Computation
, 5, 2353–2370, 2009, NIHMSID 140829, PMC2757763.
159. 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
160. Burkhard, K., Smith, S., Deshmukh, R., MacKerell, A.D. Jr., Shapiro, P., “Development of extracellular signal-regulated kinase inhibitors,” Current Topics in Medicinal Chemistry,
161. 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,
162. Vanommeslaeghe, K. Hatcher, E., Acharya, C., Kundu, S. Zhong, S., Shim, J., E. Darian, E., Guvench, O., Lopes, P., Vorobyov, I., MacKerell, A.D., Jr., “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.
163. 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, A.D., Jr. , 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, PMC2858395
164. 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, PMC2824916
165. 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
166. Yu, H., Whitfield, T.W., Harder, E., Lamoureux, G., Vorobyov, I., Anisimov, V. M., MacKerell, A.D., Jr., 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, PMC2838399
167. 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, PMC2853947
168. Klauda, J.B., Venable, R.M., Freites, J.A., O’Connor, J.W., Tobias, D.J. Mondragon- Ramirez, C., , 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, PMC2922408
169. 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, PMC2891776.
170. 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, PMC2915899.
171. 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., 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, PMC2995924.
172. Semenyuk, A., Darian, E., Liu, J., Majumdar, A., Cuenoud, B., Miller, P., MacKerell,Jr., A.D., Seidman, M. "Targeting of an interrupted Polypurine:Polypyrimidine sequence in a Triplex forming oligonucleotide containing a novel base analog," Biochemistry, 49: 7867-
173. 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
174. Xibing He, X., Olgun Guvench, O., Alexander D. MacKerell Jr., A.D., and Michael L. Klein, M.L. “Atomistic Simulation Study of Linear Alkylbenzene Sulfonates at The
Water/Air Interface,” Journal of Physical Chemistry B, 114: 9787-9794, 2010,
PMC2924668
175. 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, PMC2958709
176. West, A.L., St. John, F., Lopes, P.E.M., MacKerell, Jr., A.D., Pozharski, E. and Sarah L.J. 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,
PMC2958704
177. Venable, R.M., Hatcher, E., Guvench, O, MacKerell, Jr., A.D., and Pastor, R.W. Journal of Physical Chemistry B, 114: 12501–12507, 2010,
NIHMSID #272317
178. Rais, R., Acharya, C., MacKerell, Jr., A.D., Polli, J., "Structural Determinants for Transport Across the Intestinal Bile Acid Transporter Using C-24 Bile Acid Conjugates" Molecular
Pharmaceutics
, 7:2240-2254, 2010, PMC2997912
179. Hatcher, E., Säwén, E., Widmalm, G., * and MacKerell, Jr., A.D.* “Conformational  altoside and Methyl α- and β-cellobioside disaccharides,” Journal
of Physical Chemistry B, 115: 597-608, 2011, NIHMSID #258949
180. Abel, S., Dupradeau, F.-Y., Raman, E.P., MacKerell, Jr., A.D. and Marchi, M., “Molecular 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
181. 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
182. 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, EPUB, 2010 183. 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, EPUB, 2010, DOI:
10.1021/ml1002184
184. 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 185. Jiang, W., Hardy, D., Phillips, J., MacKerell, Jr., A.D., Schulten, K., 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.
186. Boston, S.R., Deshmukh, R., Strome, S., Priyakumar, U.D., MacKerell Jr., A.D., and Paul Shapiro, P. “Characterization of ERK Docking Domain Inhibitors that Induce Apoptosis by
Targeting Rsk-1 and Caspase-9,” BMC Cancer, 11: 7, 2011, PMC3025971
187. 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, In Press, 2011,
188. 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, In Press, 2011, NIHMSID #263852
189. 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
, In Press, 2011
190. 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, In Press,
2011, NIHMSID # 275470
191. Pastor, R.W. and MacKerell, Jr., A.D., “Development of the CHARMM Force Field for Lipids,” Journal of Physical Chemistry Letters, Invited Perspective, In Press, 2011
192. 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, In
Press.
193. 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), ASAP, 2011.
194. Shim, J., and MacKerell Jr., A.D. “Computational ligand-based rational design: Role of conformational sampling and force fields in model development,” Med. Chem. Commun.,
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., AlanR. 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, A., 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, Editors, 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, Editors, 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, Editors, 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,
Editors, Marcel Dekker Inc., New York, 441-463, 2001.
12. MacKerell, A.D., Jr., “Interatomic Potentials: Molecules,” In Handbook of Materials
Modeling, S. Yip, Editor, Lancaster Publishing Services, Lancaster, UK, 2005
13. MacKerell, A.D., Jr., “Empirical Force Fields,” In Computational Methods for Protein
Structure Prediction and Modeling I: Basic Characterization, Ying Xu, Dong Xu, Jie
Liang, Editors, Springer, New York, In Press
14. MacKerell, A.D., Jr. 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, A.D., Jr., “Comparison of protein force fields for molecular dynamics simulations,” In Molecular Modeling of Proteins, A. Kukol, Editor, Humana
Press. 2008 (Methods Mol Biol. 2008;443:63-88. PMID: 18446282)
16. Klauda, J.B., Venable, R.M., MacKerell, Jr., A.D. and Pastor, R.W. “Considerations for Lipid Force Field Development,” In Computational Modeling of Membrane Bilayers, S. Feller,
Editor, Elsevier, Inc. Chapter, 1, 2008.
17. Priyakumar, U.D. and MacKerell, Jr., A.D., “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
18. Lopes, P.E.M, Harder, E., Roux, B., and MacKerell, Jr., A.D. “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 Computational Biochemistry and Biophysics, O. Becker, A.D. MacKerell, Jr., B. Roux and M.
Watanabe, Editors, Marcel Dekker Inc., New York, 2001.

Source: http://mackerell.umaryland.edu/Publications_files/mackerell_pubs_5-2011.pdf

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