SEARCH

SEARCH BY CITATION

Cited in:

CrossRef

This article has been cited by:

  1. 1
    Omar Demerdash, Eng-Hui Yap, Teresa Head-Gordon, Advanced Potential Energy Surfaces for Condensed Phase Simulation, Annual Review of Physical Chemistry, 2014, 65, 1, 149

    CrossRef

  2. 2
    A. Leif Hickey, Christopher N. Rowley, Benchmarking Quantum Chemical Methods for the Calculation of Molecular Dipole Moments and Polarizabilities, The Journal of Physical Chemistry A, 2014, 118, 20, 3678

    CrossRef

  3. 3
    G. Andrés Cisneros, Mikko Karttunen, Pengyu Ren, Celeste Sagui, Classical Electrostatics for Biomolecular Simulations, Chemical Reviews, 2014, 114, 1, 779

    CrossRef

  4. 4
    Nengjie Zhou, Zhenyu Lu, Qin Wu, Yingkai Zhang, Improved parameterization of interatomic potentials for rare gas dimers with density-based energy decomposition analysis, The Journal of Chemical Physics, 2014, 140, 21, 214117

    CrossRef

  5. 5
    Konstantin Lorenzen, Christoph Wichmann, Paul Tavan, Including the Dispersion Attraction into Structure-Adapted Fast Multipole Expansions for MD Simulations, Journal of Chemical Theory and Computation, 2014, 10, 8, 3244

    CrossRef

  6. 6
    Jing Huang, Alexander D. MacKerell, Induction of Peptide Bond Dipoles Drives Cooperative Helix Formation in the (AAQAA)3 Peptide, Biophysical Journal, 2014, 107, 4, 991

    CrossRef

  7. 7
    Cui Liu, Yang Wang, Dongxia Zhao, Lidong Gong, Zhongzhi Yang, Investigation of base pairs containing oxidized guanine using ab initio method and ABEEMσπ polarizable force field, Journal of Molecular Graphics and Modelling, 2014, 47, 62

    CrossRef

  8. 8
    Thibaud Etienne, Xavier Assfeld, Antonio Monari, QM/MM calculation of absorption spectra of complex systems: The case of human serum albumin, Computational and Theoretical Chemistry, 2014, 1040-1041, 360

    CrossRef

  9. 9
    Jing Huang, Pedro E. M. Lopes, Benoît Roux, Alexander D. MacKerell, Recent Advances in Polarizable Force Fields for Macromolecules: Microsecond Simulations of Proteins Using the Classical Drude Oscillator Model, The Journal of Physical Chemistry Letters, 2014, 3144

    CrossRef

  10. 10
    Soroosh Pezeshki, Hai Lin, Recent developments in QM/MM methods towards open-boundary multi-scale simulations, Molecular Simulation, 2014, 1

    CrossRef

  11. 11
    Hari S. Muddana, Neil V. Sapra, Andrew T. Fenley, Michael K. Gilson, The SAMPL4 hydration challenge: evaluation of partial charge sets with explicit-water molecular dynamics simulations, Journal of Computer-Aided Molecular Design, 2014, 28, 3, 277

    CrossRef

  12. 12
    Zhong-Zhi Yang, Jian-Jiang Wang, Dong-Xia Zhao, Valence state parameters of all transition metal atoms in metalloproteins—development of ABEEMσπ fluctuating charge force field, Journal of Computational Chemistry, 2014, 35, 23
  13. 13
    Janamejaya Chowdhary, Edward Harder, Pedro E. M. Lopes, Lei Huang, Alexander D. MacKerell, Benoît Roux, A Polarizable Force Field of Dipalmitoylphosphatidylcholine Based on the Classical Drude Model for Molecular Dynamics Simulations of Lipids, The Journal of Physical Chemistry B, 2013, 117, 31, 9142

    CrossRef

  14. 14
    T. Verstraelen, P. W. Ayers, V. Van Speybroeck, M. Waroquier, ACKS2: Atom-condensed Kohn-Sham DFT approximated to second order, The Journal of Chemical Physics, 2013, 138, 7, 074108

    CrossRef

  15. 15
    Anna Stachowicz, Marek Rogalski, Jacek Korchowiec, Charge sensitivity approach to mutual polarization of reactants: molecular mechanics perspective, Journal of Molecular Modeling, 2013, 19, 10, 4163

    CrossRef

  16. 16
    Xudong Xiao, Tong Zhu, Chang G. Ji, John Z. H. Zhang, Development of an Effective Polarizable Bond Method for Biomolecular Simulation, The Journal of Physical Chemistry B, 2013, 131125104347002

    CrossRef

  17. 17
    Keith McLaughlin, Christian R. Cioce, Tony Pham, Jonathan L. Belof, Brian Space, Efficient calculation of many-body induced electrostatics in molecular systems, The Journal of Chemical Physics, 2013, 139, 18, 184112

    CrossRef

  18. 18
    Steven K. Burger, G. Andrés Cisneros, Efficient optimization of van der Waals parameters from bulk properties, Journal of Computational Chemistry, 2013, 34, 27
  19. You have free access to this content19
    Art D. Bochevarov, Edward Harder, Thomas F. Hughes, Jeremy R. Greenwood, Dale A. Braden, Dean M. Philipp, David Rinaldo, Mathew D. Halls, Jing Zhang, Richard A. Friesner, Jaguar: A high-performance quantum chemistry software program with strengths in life and materials sciences, International Journal of Quantum Chemistry, 2013, 113, 18
  20. 20
    Tiedong Sun, Caiyi Wei, Ni Wei Charlie Neo, Dawei Zhang, Misfolding of a polyalanine variant due to lack of electrostatic polarization effects, Theoretical Chemistry Accounts, 2013, 132, 5

    CrossRef

  21. 21
    Yue Shi, Zhen Xia, Jiajing Zhang, Robert Best, Chuanjie Wu, Jay W. Ponder, Pengyu Ren, Polarizable Atomic Multipole-Based AMOEBA Force Field for Proteins, Journal of Chemical Theory and Computation, 2013, 9, 9, 4046

    CrossRef

  22. 22
    Pedro E. M. Lopes, Jing Huang, Jihyun Shim, Yun Luo, Hui Li, Benoît Roux, Alexander D. MacKerell, Polarizable Force Field for Peptides and Proteins Based on the Classical Drude Oscillator, Journal of Chemical Theory and Computation, 2013, 9, 12, 5430

    CrossRef

  23. 23
    Xinbi Li, Sergei Y. Ponomarev, Qina Sa, Daniel L. Sigalovsky, George A. Kaminski, Polarizable simulations with second order interaction model (POSSIM) force field: Developing parameters for protein side-chain analogues, Journal of Computational Chemistry, 2013, 34, 14
  24. 24
    Steven K. Burger, Jeremy Schofield, Paul W. Ayers, Quantum Mechanics/Molecular Mechanics Restrained Electrostatic Potential Fitting, The Journal of Physical Chemistry B, 2013, 131121105224004

    CrossRef

  25. 25
    Franziska Hoffgaard, Jochen Heil, Stefan M. Kast, Three-Dimensional RISM Integral Equation Theory for Polarizable Solute Models, Journal of Chemical Theory and Computation, 2013, 9, 11, 4718

    CrossRef

  26. 26
    Toon Verstraelen, Ewald Pauwels, Frank De Proft, Veronique Van Speybroeck, Paul Geerlings, Michel Waroquier, Assessment of Atomic Charge Models for Gas-Phase Computations on Polypeptides, Journal of Chemical Theory and Computation, 2012, 8, 2, 661

    CrossRef

  27. 27
    Pengyu Ren, Jaehun Chun, Dennis G. Thomas, Michael J. Schnieders, Marcelo Marucho, Jiajing Zhang, Nathan A. Baker, Biomolecular electrostatics and solvation: a computational perspective, Quarterly Reviews of Biophysics, 2012, 45, 04, 427

    CrossRef

  28. 28
    Victor M. Anisimov, Andrey A. Bliznyuk, Charge Transfer Effects in the GroEL–GroES Chaperonin Tetramer in Solution, The Journal of Physical Chemistry B, 2012, 116, 22, 6261

    CrossRef

  29. 29
    Cui Liu, Dong-Xia Zhao, Zhong-Zhi Yang, Direct evaluation of individual hydrogen bond energy in situ in intra- and intermolecular multiple hydrogen bonds system, Journal of Computational Chemistry, 2012, 33, 4
  30. 30
    Sergei Y. Ponomarev, Qina Sa, George A. Kaminski, Effects of Lysine Substitution on Stability of Polyalanine α Helix, Journal of Chemical Theory and Computation, 2012, 8, 11, 4691

    CrossRef

  31. 31
    Guillaume Lamoureux, Esam A. Orabi, Molecular modelling of cation–π interactions, Molecular Simulation, 2012, 38, 8-9, 704

    CrossRef

  32. 32
    Hyun Woo Kim, Young Min Rhee, Molecule-specific determination of atomic polarizabilities with the polarizable atomic multipole model, Journal of Computational Chemistry, 2012, 33, 20
  33. 33
    Michael Y. Patuwo, Ryan P.A. Bettens, Monte Carlo simulation of several biologically relevant molecules and zwitterions in water, Chemical Physics Letters, 2012, 524, 90

    CrossRef

  34. 34
    Tugba G. Kucukkal, Steven J. Stuart, Polarizable Molecular Dynamics Simulations of Aqueous Dipeptides, The Journal of Physical Chemistry B, 2012, 116, 30, 8733

    CrossRef

  35. 35
    Kshatresh Dutta Dubey, Amit Kumar Chaubey, Rajendra Prasad Ojha, Role of polarization in ligand docking and binding affinity prediction for inhibitors of dengue virus, Medicinal Chemistry Research, 2012, 21, 7, 1030

    CrossRef

  36. 36
    Eliot Boulanger, Walter Thiel, Solvent Boundary Potentials for Hybrid QM/MM Computations Using Classical Drude Oscillators: A Fully Polarizable Model, Journal of Chemical Theory and Computation, 2012, 8, 11, 4527

    CrossRef

  37. 37
    R.C. de Berrêdo, F.E. Jorge, Sara S. Jorge, R. Centoducatte, An augmented Gaussian basis set for calculations of molecular polarizabilities on platinum compounds, Computational and Theoretical Chemistry, 2011, 965, 1, 236

    CrossRef

  38. 38
    Bryce Devine, Tzu-Ray Shan, Yu-Ting Cheng, Alan J. H. McGaughey, Minyoung Lee, Simon R. Phillpot, Susan B. Sinnott, Atomistic simulations of copper oxidation and Cu/Cu_{2}O interfaces using charge-optimized many-body potentials, Physical Review B, 2011, 84, 12

    CrossRef

  39. 39
    Miho Isegawa, Jiali Gao, Donald G. Truhlar, Incorporation of charge transfer into the explicit polarization fragment method by grand canonical density functional theory, The Journal of Chemical Physics, 2011, 135, 8, 084107

    CrossRef

  40. 40
    Pengyu Ren, Chuanjie Wu, Jay W. Ponder, Polarizable Atomic Multipole-Based Molecular Mechanics for Organic Molecules, Journal of Chemical Theory and Computation, 2011, 7, 10, 3143

    CrossRef

  41. 41
    Sergei Y. Ponomarev, George A. Kaminski, Polarizable Simulations with Second-Order Interaction Model (POSSIM) Force Field: Developing Parameters for Alanine Peptides and Protein Backbone, Journal of Chemical Theory and Computation, 2011, 7, 5, 1415

    CrossRef

  42. 42
    F. Javier Luque, François Dehez, Christophe Chipot, Modesto Orozco, Polarization effects in molecular interactions, Wiley Interdisciplinary Reviews: Computational Molecular Science, 2011, 1, 5
  43. 43
    Yaoqi Zhou, Yong Duan, Yuedong Yang, Eshel Faraggi, Hongxing Lei, Trends in template/fragment-free protein structure prediction, Theoretical Chemistry Accounts, 2011, 128, 1, 3

    CrossRef

  44. 44
    Hiroshi Nakano, Takeshi Yamamoto, Shigeki Kato, A wave-function based approach for polarizable charge model: Systematic comparison of polarization effects on protic, aprotic, and ionic liquids, The Journal of Chemical Physics, 2010, 132, 4, 044106

    CrossRef

  45. 45
    CUI LIU, DONG-XIA ZHAO, ZHONG-ZHI YANG, ABEEMσπ FLUCTUATING CHARGE FORCE FIELD APPLIED TO ALANINE DIPEPTIDE AND ALANINE DIPEPTIDE–WATER SYSTEMS, Journal of Theoretical and Computational Chemistry, 2010, 09, supp01, 77

    CrossRef

  46. 46
    Yunpeng Lu, Ye Mei, John Z. H. Zhang, Dawei Zhang, Communications: Electron polarization critically stabilizes the Mg[sup 2+] complex in the catalytic core domain of HIV-1 integrase, The Journal of Chemical Physics, 2010, 132, 13, 131101

    CrossRef

  47. 47
    Yan Tong, Ye Mei, Yong L. Li, Chang G. Ji, John Z. H. Zhang, Electrostatic Polarization Makes a Substantial Contribution to the Free Energy of Avidin−Biotin Binding, Journal of the American Chemical Society, 2010, 132, 14, 5137

    CrossRef

  48. 48
    Kara E. Ranaghan, Adrian J. Mulholland, Investigations of enzyme-catalysed reactions with combined quantum mechanics/molecular mechanics (QM/MM) methods, International Reviews in Physical Chemistry, 2010, 29, 1, 65

    CrossRef

  49. 49
    N.M. Garrido, A.J. Queimada, M. Jorge, I.G. Economou, E.A. Macedo, Molecular simulation of absolute hydration Gibbs energies of polar compounds, Fluid Phase Equilibria, 2010, 296, 2, 110

    CrossRef

  50. 50
    Jean-François Truchon, Anthony Nicholl's, J. Andrew Grant, Radu I. Iftimie, Benoît Roux, Christopher I. Bayly, Using electronic polarization from the internal continuum (EPIC) for intermolecular interactions, Journal of Computational Chemistry, 2010, 31, 4
  51. 51
    A Mayer, A L González, C M Aikens, G C Schatz, A charge–dipole interaction model for the frequency-dependent polarizability of silver clusters, Nanotechnology, 2009, 20, 19, 195204

    CrossRef

  52. 52
    Jia-Wei Shen, Tao Wu, Qi Wang, Yu Kang, Xin Chen, Adsorption of Insulin Peptide on Charged Single-Walled Carbon Nanotubes: Significant Role of Ordered Water Molecules, ChemPhysChem, 2009, 10, 8
  53. 53
    Hao Hu, Weitao Yang, Development and application of ab initio QM/MM methods for mechanistic simulation of reactions in solution and in enzymes, Journal of Molecular Structure: THEOCHEM, 2009, 898, 1-3, 17

    CrossRef

  54. 54
    A Mayer, G C Schatz, Enhanced polarizability of aromatic molecules placed in the vicinity of silver clusters, Journal of Physics: Condensed Matter, 2009, 21, 32, 325301

    CrossRef

  55. 55
    Yohsuke Hagiwara, Hiroyoshi Matsumura, Masaru Tateno, Functional Roles of a Structural Element Involving Na+-π Interactions in the Catalytic Site of T1 Lipase Revealed by Molecular Dynamics Simulations, Journal of the American Chemical Society, 2009, 131, 46, 16697

    CrossRef

  56. 56
    M. Souaille, H. Loirat, D. Borgis, M.P. Gaigeot, MDVRY: a polarizable classical molecular dynamics package for biomolecules, Computer Physics Communications, 2009, 180, 2, 276

    CrossRef

  57. 57
    B. R. Meher, M. V. Satish Kumar, Pradipta Bandyopadhyay, Molecular dynamics simulation of HIV-protease with polarizable and non-polarizable force fields, Indian Journal of Physics, 2009, 83, 1, 81

    CrossRef

  58. 58
    Pedro E. M. Lopes, Benoit Roux, Alexander D. MacKerell, Molecular modeling and dynamics studies with explicit inclusion of electronic polarizability: theory and applications, Theoretical Chemistry Accounts, 2009, 124, 1-2, 11

    CrossRef

  59. 59
    Hans S. Smalo̸, Per-Olof Åstrand, Lasse Jensen, Nonmetallic electronegativity equalization and point-dipole interaction model including exchange interactions for molecular dipole moments and polarizabilities, The Journal of Chemical Physics, 2009, 131, 4, 044101

    CrossRef

  60. 60
    Qiang Zhang, Xia Zhang, Long Yu, Dong-Xia Zhao, Polarizable force field for water–dimethyl sulfoxide systems: I Parameterization and gas phase test, Journal of Molecular Liquids, 2009, 145, 2, 58

    CrossRef

  61. 61
    Piotr Cieplak, François-Yves Dupradeau, Yong Duan, Junmei Wang, Polarization effects in molecular mechanical force fields, Journal of Physics: Condensed Matter, 2009, 21, 33, 333102

    CrossRef

  62. 62
    Hans Martin Senn, Walter Thiel, QM/MM Methods for Biomolecular Systems, Angewandte Chemie International Edition, 2009, 48, 7
  63. 63
    Hans Martin Senn, Walter Thiel, QM/MM-Methoden für biomolekulare Systeme, Angewandte Chemie, 2009, 121, 7
  64. 64
    A Mayer, Ph Lambin, P-O Åstrand, An electrostatic interaction model for frequency-dependent polarizability: methodology and applications to hydrocarbons and fullerenes, Nanotechnology, 2008, 19, 2, 025203

    CrossRef

  65. 65
    O. Khoruzhii, A. G. Donchev, N. Galkin, A. Illarionov, M. Olevanov, V. Ozrin, C. Queen, V. Tarasov, Application of a polarizable force field to calculations of relative protein-ligand binding affinities, Proceedings of the National Academy of Sciences, 2008, 105, 30, 10378

    CrossRef

  66. 66
    Alexander G. Donchev, Nikolay G. Galkin, Alexey A. Illarionov, Oleg V. Khoruzhii, Michael A. Olevanov, Vladimir D. Ozrin, Leonid B. Pereyaslavets, Vladimir I. Tarasov, Assessment of performance of the general purpose polarizable force field QMPFF3 in condensed phase, Journal of Computational Chemistry, 2008, 29, 8
  67. 67
    M. W van der Kamp, K. E Shaw, C. J Woods, A. J Mulholland, Biomolecular simulation and modelling: status, progress and prospects, Journal of The Royal Society Interface, 2008, 5, Suppl_3, 173

    CrossRef

  68. 68
    Liqiang Chen, Riccardo Petrelli, Magdalena Olesiak, Daniel J. Wilson, Nicholas P. Labello, Krzysztof W. Pankiewicz, Bis(sulfonamide) isosters of mycophenolic adenine dinucleotide analogues: Inhibition of inosine monophosphate dehydrogenase, Bioorganic & Medicinal Chemistry, 2008, 16, 15, 7462

    CrossRef

  69. 69
    J. Kirkpatrick, V. Marcon, K. Kremer, J. Nelson, D. Andrienko, Charge transport parameters of HBC at different temperatures, physica status solidi (b), 2008, 245, 5
  70. 70
    Brad A. Bauer, Sandeep Patel, Condensed-phase properties of n-alkyl-amines from molecular dynamics simulations using charge equilibration force fields, Journal of Molecular Liquids, 2008, 142, 1-3, 32

    CrossRef

  71. 71
    David C. Thompson, R. Aldrin Denny, Ramaswamy Nilakantan, Christine Humblet, Diane Joseph-McCarthy, Eric Feyfant, CONFIRM: connecting fragments found in receptor molecules, Journal of Computer-Aided Molecular Design, 2008, 22, 10, 761

    CrossRef

  72. 72
    Changge Ji, Ye Mei, John Z.H. Zhang, Developing Polarized Protein-Specific Charges for Protein Dynamics: MD Free Energy Calculation of pKa Shifts for Asp26/Asp20 in Thioredoxin, Biophysical Journal, 2008, 95, 3, 1080

    CrossRef

  73. 73
    Salvatore Millefiori, Andrea Alparone, Arcangelo Millefiori, Angelo Vanella, Electronic and vibrational polarizabilities of the twenty naturally occurring amino acids, Biophysical Chemistry, 2008, 132, 2-3, 139

    CrossRef

  74. 74
    F. Calvo, P. Dugourd, Folding of Gas-Phase Polyalanines in a Static Electric Field: Alignment, Deformations, and Polarization Effects, Biophysical Journal, 2008, 95, 1, 18

    CrossRef

  75. 75
    Kalju Kahn, Iiris Kahn, Improved efficiency of focal point conformational analysis with truncated correlation consistent basis sets, Journal of Computational Chemistry, 2008, 29, 6
  76. 76
    Robert A. Latour, Molecular simulation of protein-surface interactions: Benefits, problems, solutions, and future directions (Review), Biointerphases, 2008, 3, 3, FC2

    CrossRef

  77. 77
    Liqiang Chen, Daniel J. Wilson, Nicholas P. Labello, Hiremagalur N. Jayaram, Krzysztof W. Pankiewicz, Mycophenolic acid analogs with a modified metabolic profile, Bioorganic & Medicinal Chemistry, 2008, 16, 20, 9340

    CrossRef

  78. 78
    Lochana C. Menikarachchi, José A. Gascón, Optimization of cutting schemes for the evaluation of molecular electrostatic potentials in proteins via Moving-Domain QM/MM, Journal of Molecular Modeling, 2008, 14, 6, 1

    CrossRef

  79. 79
    G. Lee Warren, Joseph E. Davis, Sandeep Patel, Origin and control of superlinear polarizability scaling in chemical potential equalization methods, The Journal of Chemical Physics, 2008, 128, 14, 144110

    CrossRef

  80. 80
    Dennis Elking, Tom Darden, Robert J. Woods, Gaussian induced dipole polarization model, Journal of Computational Chemistry, 2007, 28, 7
  81. 81
    Anna Jagielska, Jeffrey Skolnick, Origin of intrinsic 310-helix versus strand stability in homopolypeptides and its implications for the accuracy of the Amber force field, Journal of Computational Chemistry, 2007, 28, 10
  82. 82
    Setsuko Nakagawa, Polarizable model potential function for nucleic acid bases, Journal of Computational Chemistry, 2007, 28, 9
  83. 83
    Hongxing Lei, Yong Duan, Two-stage Folding of HP-35 from Ab Initio Simulations, Journal of Molecular Biology, 2007, 370, 1, 196

    CrossRef

  84. 84
    M. Swart, P.Th. van Duijnen, DRF90: a polarizable force field, Molecular Simulation, 2006, 32, 6, 471

    CrossRef

  85. 85
    Patrice Koehl, Electrostatics calculations: latest methodological advances, Current Opinion in Structural Biology, 2006, 16, 2, 142

    CrossRef

  86. 86
    Sandeep Patel, Charles L. Brooks, Fluctuating charge force fields: recent developments and applications from small molecules to macromolecular biological systems, Molecular Simulation, 2006, 32, 3-4, 231

    CrossRef

  87. 87
    T. Liang, T. R. Walsh, Molecular dynamics simulations of peptide carboxylate hydration, Physical Chemistry Chemical Physics, 2006, 8, 38, 4410

    CrossRef

  88. 88
    Denis Bucher, Simone Raugei, Leonardo Guidoni, Matteo Dal Peraro, Ursula Rothlisberger, Paolo Carloni, Michael L. Klein, Polarization effects and charge transfer in the KcsA potassium channel, Biophysical Chemistry, 2006, 124, 3, 292

    CrossRef

  89. 89
    Zhi-Xiang Wang, Wei Zhang, Chun Wu, Hongxing Lei, Piotr Cieplak, Yong Duan, Strike a balance: Optimization of backbone torsion parameters of AMBER polarizable force field for simulations of proteins and peptides, Journal of Computational Chemistry, 2006, 27, 6
  90. 90
    Zhong-Zhi Yang, Qiang Zhang, Study of peptide conformation in terms of the ABEEM/MM method, Journal of Computational Chemistry, 2006, 27, 1
  91. 91
    K. J. Jalkanen, V. Würtz Jürgensen, A. Claussen, A. Rahim, G. M. Jensen, R. C. Wade, F. Nardi, C. Jung, I. M. Degtyarenko, R. M. Nieminen, F. Herrmann, M. Knapp-Mohammady, T. A. Niehaus, K. Frimand, S. Suhai, Use of vibrational spectroscopy to study protein and DNA structure, hydration, and binding of biomolecules: A combined theoretical and experimental approach, International Journal of Quantum Chemistry, 2006, 106, 5
  92. 92
    D Elking, R Woods, T Darden, Recent Progress in Computational Sciences and Engineering (2 vols), 2006,

    CrossRef

  93. 93
    Chang-Sheng Wang, Yan Zhang, Kun Gao, Zhong-Zhi Yang, A new scheme for determining the intramolecular seven-membered ring N–H⋯O[Double Bond]C hydrogen-bonding energies of glycine and alanine peptides, The Journal of Chemical Physics, 2005, 123, 2, 024307

    CrossRef

  94. 94
    A. G. Donchev, V. D. Ozrin, M. V. Subbotin, O. V. Tarasov, V. I. Tarasov, A quantum mechanical polarizable force field for biomolecular interactions, Proceedings of the National Academy of Sciences, 2005, 102, 22, 7829

    CrossRef

  95. 95
    Richard A. Friesner, Victor Guallar, AB INITIO QUANTUM CHEMICAL AND MIXED QUANTUM MECHANICS/MOLECULAR MECHANICS (QM/MM) METHODS FOR STUDYING ENZYMATIC CATALYSIS, Annual Review of Physical Chemistry, 2005, 56, 1, 389

    CrossRef

  96. 96
    R. A. Friesner, Ab initio quantum chemistry: Methodology and applications, Proceedings of the National Academy of Sciences, 2005, 102, 19, 6648

    CrossRef

  97. 97
    Nicholas P. Labello, Antonio M. Ferreira, Henry A. Kurtz, An augmented effective core potential basis set for the calculation of molecular polarizabilities, Journal of Computational Chemistry, 2005, 26, 14
  98. 98
    F. Wennmohs, M. Schindler, Development of a multipoint model for sulfur in proteins: A new parametrization scheme to reproduce high-level ab initio interaction energies, Journal of Computational Chemistry, 2005, 26, 3
  99. 99
    Kalju Kahn, Thomas C. Bruice, Focal-Point Conformational Analysis of Ethanol, Propanol, and Isopropanol, ChemPhysChem, 2005, 6, 3
  100. 100
    Jay L. Banks, Hege S. Beard, Yixiang Cao, Art E. Cho, Wolfgang Damm, Ramy Farid, Anthony K. Felts, Thomas A. Halgren, Daniel T. Mainz, Jon R. Maple, Robert Murphy, Dean M. Philipp, Matthew P. Repasky, Linda Y. Zhang, Bruce J. Berne, Richard A. Friesner, Emilio Gallicchio, Ronald M. Levy, Integrated Modeling Program, Applied Chemical Theory (IMPACT), Journal of Computational Chemistry, 2005, 26, 16
  101. 101
    Ran Friedman, Esther Nachliel, Menachem Gutman, Molecular Dynamics of a Protein Surface: Ion-Residues Interactions, Biophysical Journal, 2005, 89, 2, 768

    CrossRef

  102. 102
    I.V. Leontyev, A.V. Tovmash, M.V. Vener, I.V. Rostov, M.V. Basilevsky, Molecular simulations of outersphere reorganization energies for intramolecular electron and hole transfer in polar solvents, Chemical Physics, 2005, 319, 1-3, 4

    CrossRef

  103. 103
    Riccardo Chelli, Marco Pagliai, Piero Procacci, Gianni Cardini, Vincenzo Schettino, Polarization response of water and methanol investigated by a polarizable force field and density functional theory calculations: Implications for charge transfer, The Journal of Chemical Physics, 2005, 122, 7, 074504

    CrossRef

  104. 104
    I. V. Leontyev, M. Tachiya, The reorganization energy of electron transfer in nonpolar solvents: Molecular level treatment of the solvent, The Journal of Chemical Physics, 2005, 123, 22, 224502

    CrossRef

  105. 105
    Alexander D. MacKerell, 2005,

    CrossRef

  106. 106
    Richard A. Friesner, Peptide Solvation and H-Bonds, 2005,

    CrossRef

  107. 107
    Song Liu, Chi Zhang, Hongyi Zhou, Yaoqi Zhou, A physical reference state unifies the structure-derived potential of mean force for protein folding and binding, Proteins: Structure, Function, and Bioinformatics, 2004, 56, 1
  108. 108
    Robert W. Williams, Ian Bone, Alan F. Weir, A scaled quantum mechanical force field for the alanine–alanine zwitterions in water based on scale factors for alanine, glycine, N-methylacetamide, acetate, formate, and methylamine, Journal of Molecular Structure, 2004, 697, 1-3, 81

    CrossRef

  109. 109
    Sandeep Patel, Charles L. Brooks, CHARMM fluctuating charge force field for proteins: I parameterization and application to bulk organic liquid simulations, Journal of Computational Chemistry, 2004, 25, 1
  110. 110
    Sandeep Patel, Alexander D. Mackerell, Charles L. Brooks, CHARMM fluctuating charge force field for proteins: II Protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model, Journal of Computational Chemistry, 2004, 25, 12
  111. 111
    A. V. Morozov, T. Kortemme, K. Tsemekhman, D. Baker, Close agreement between the orientation dependence of hydrogen bonds observed in protein structures and quantum mechanical calculations, Proceedings of the National Academy of Sciences, 2004, 101, 18, 6946

    CrossRef

  112. 112
    Richard A. Friesner, Combined quantum and molecular mechanics (QM/MM), Drug Discovery Today: Technologies, 2004, 1, 3, 253

    CrossRef

  113. 113
    Alexander D. Mackerell, Empirical force fields for biological macromolecules: Overview and issues, Journal of Computational Chemistry, 2004, 25, 13
  114. 114
    Nohad Gresh, Sherif A. Kafafi, Jean-François Truchon, Dennis R. Salahub, Intramolecular interaction energies in model alanine and glycine tetrapeptides. Evaluation of anisotropy, polarization, and correlation effects. A parallel ab initio HF/MP2, DFT, and polarizable molecular mechanics study, Journal of Computational Chemistry, 2004, 25, 6
  115. 115
    Marco Masia, Michael Probst, Rossend Rey, On the performance of molecular polarization methods. I. Water and carbon tetrachloride close to a point charge, The Journal of Chemical Physics, 2004, 121, 15, 7362

    CrossRef

  116. 116
    Hui Li, Andrew D. Robertson, Jan H. Jensen, The determinants of carboxyl pKa values in turkey ovomucoid third domain, Proteins: Structure, Function, and Bioinformatics, 2004, 55, 3
  117. 117
    Kim Palmo, Samuel Krimm, Theoretical basis and accuracy of a non-iterative polarization protocol in molecular mechanics energy function calculations, Chemical Physics Letters, 2004, 395, 1-3, 133

    CrossRef

  118. 118
    Yong Duan, Chun Wu, Shibasish Chowdhury, Mathew C. Lee, Guoming Xiong, Wei Zhang, Rong Yang, Piotr Cieplak, Ray Luo, Taisung Lee, James Caldwell, Junmei Wang, Peter Kollman, A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations, Journal of Computational Chemistry, 2003, 24, 16
  119. 119
    Philippe Huetz, Christophe Ramseyer, Claude Girardet, Ab initio study of the influence of conformation on partial charge distribution of dioctadecylamine, Chemical Physics Letters, 2003, 380, 3-4, 424

    CrossRef

  120. 120
    Jean-Philip Piquemal, Ben Williams-Hubbard, Natalie Fey, Robert J. Deeth, Nohad Gresh, Claude Giessner-Prettre, Inclusion of the ligand field contribution in a polarizable molecular mechanics: SIBFA-LF, Journal of Computational Chemistry, 2003, 24, 16
  121. 121
    Markus Reiher, Dirk Bakowies, Martin Schütz, Theoretische Chemie 2002, Nachrichten aus der Chemie, 2003, 51, 3
  122. 122
    Irwin D Kuntz, David A Agard, Protein Simulations, 2003,

    CrossRef

  123. 123
    Jay W. Ponder, David A. Case, Protein Simulations, 2003,

    CrossRef

  124. 124
    Paul Tavan, Heiko Carstens, Gerald Mathias, Molecular Dynamics Simulations of Proteins and Peptides, Protein Science Encyclopedia,