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Volumn 119, Issue 32, 2015, Pages 10145-10155

Toward Improved Force-Field Accuracy through Sensitivity Analysis of Host-Guest Binding Thermodynamics

Author keywords

[No Author keywords available]

Indexed keywords

BINDING ENERGY; LIGANDS; PROTEINS; THERMODYNAMICS;

EID: 84939228881     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/acs.jpcb.5b04262     Document Type: Article
Times cited : (31)

References (115)
  • 1
    • 3142716857 scopus 로고    scopus 로고
    • Accelerated Molecular Dynamics: A Promising and Efficient Simulation Method for Biomolecules
    • Hamelberg, D.; Mongan, J.; McCammon, J. A. Accelerated Molecular Dynamics: A Promising and Efficient Simulation Method for Biomolecules J. Chem. Phys. 2004, 120, 11919-11929 10.1063/1.1755656
    • (2004) J. Chem. Phys. , vol.120 , pp. 11919-11929
    • Hamelberg, D.1    Mongan, J.2    McCammon, J.A.3
  • 2
    • 0037157317 scopus 로고    scopus 로고
    • On the Hamiltonian Replica Exchange Method for Efficient Sampling of Biomolecular Systems: Application to Protein Structure Prediction
    • Fukunishi, H.; Watanabe, O.; Takada, S. On the Hamiltonian Replica Exchange Method for Efficient Sampling of Biomolecular Systems: Application to Protein Structure Prediction J. Chem. Phys. 2002, 116, 9058-9067 10.1063/1.1472510
    • (2002) J. Chem. Phys. , vol.116 , pp. 9058-9067
    • Fukunishi, H.1    Watanabe, O.2    Takada, S.3
  • 4
    • 0030819348 scopus 로고    scopus 로고
    • Multicanonical Ensemble Generated by Molecular Dynamics Simulation for Enhanced Conformational Sampling of Peptides
    • Nakajima, N.; Nakamura, H.; Kidera, A. Multicanonical Ensemble Generated by Molecular Dynamics Simulation for Enhanced Conformational Sampling of Peptides J. Phys. Chem. B 1997, 101, 817-824 10.1021/jp962142e
    • (1997) J. Phys. Chem. B , vol.101 , pp. 817-824
    • Nakajima, N.1    Nakamura, H.2    Kidera, A.3
  • 5
    • 0025600834 scopus 로고
    • Enhanced Sampling in Molecular Dynamics: Use of the Time-Dependent Hartree Approximation for a Simulation of Carbon Monoxide Diffusion through Myoglobin
    • Elber, R.; Karplus, M. Enhanced Sampling in Molecular Dynamics: Use of the Time-Dependent Hartree Approximation for a Simulation of Carbon Monoxide Diffusion through Myoglobin J. Am. Chem. Soc. 1990, 112, 9161-9175 10.1021/ja00181a020
    • (1990) J. Am. Chem. Soc. , vol.112 , pp. 9161-9175
    • Elber, R.1    Karplus, M.2
  • 6
    • 84897584647 scopus 로고    scopus 로고
    • Efficient and Unbiased Sampling of Biomolecular Systems in the Canonical Ensemble: A Review of Self-Guided Langevin Dynamics
    • Wu, X.; Damjanovic, A.; Brooks, B. Efficient and Unbiased Sampling of Biomolecular Systems in the Canonical Ensemble: A Review of Self-Guided Langevin Dynamics Adv. Chem. Phys. 2012, 150, 255-326 10.1002/9781118197714.ch6
    • (2012) Adv. Chem. Phys. , vol.150 , pp. 255-326
    • Wu, X.1    Damjanovic, A.2    Brooks, B.3
  • 7
    • 1942455272 scopus 로고    scopus 로고
    • Generalized-Ensemble Algorithms: Enhanced Sampling Techniques for Monte Carlo and Molecular Dynamics Simulations
    • Okamoto, Y. Generalized-Ensemble Algorithms: Enhanced Sampling Techniques for Monte Carlo and Molecular Dynamics Simulations J. Mol. Graphics Modell. 2004, 22, 425-439 10.1016/j.jmgm.2003.12.009
    • (2004) J. Mol. Graphics Modell. , vol.22 , pp. 425-439
    • Okamoto, Y.1
  • 8
    • 84900551635 scopus 로고    scopus 로고
    • Molecular Dynamics in the Multicanonical Ensemble: Equivalence of Wang-Landau Sampling, Statistical Temperature Molecular Dynamics, and Metadynamics
    • Junghans, C.; Perez, D.; Vogel, T. Molecular Dynamics in the Multicanonical Ensemble: Equivalence of Wang-Landau Sampling, Statistical Temperature Molecular Dynamics, and Metadynamics J. Chem. Theory Comput. 2014, 10, 1843-1847 10.1021/ct500077d
    • (2014) J. Chem. Theory Comput. , vol.10 , pp. 1843-1847
    • Junghans, C.1    Perez, D.2    Vogel, T.3
  • 9
    • 38349091489 scopus 로고    scopus 로고
    • Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method
    • Barducci, A.; Bussi, G.; Parrinello, M. Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method Phys. Rev. Lett. 2008, 100, 020603 10.1103/PhysRevLett.100.020603
    • (2008) Phys. Rev. Lett. , vol.100 , pp. 020603
    • Barducci, A.1    Bussi, G.2    Parrinello, M.3
  • 11
    • 84921469425 scopus 로고    scopus 로고
    • The Adaptive Biasing Force Method: Everything You Always Wanted to Know but Were Afraid to Ask
    • Comer, J.; Gumbart, J. C.; Hénin, J.; Lelièvre, T.; Pohorille, A.; Chipot, C. The Adaptive Biasing Force Method: Everything You Always Wanted To Know but Were Afraid To Ask J. Phys. Chem. B 2015, 119, 1129-1151 10.1021/jp506633n
    • (2015) J. Phys. Chem. B , vol.119 , pp. 1129-1151
    • Comer, J.1    Gumbart, J.C.2    Hénin, J.3    Lelièvre, T.4    Pohorille, A.5    Chipot, C.6
  • 12
    • 72449125773 scopus 로고    scopus 로고
    • Using the Local Elevation Method to Construct Optimized Umbrella Sampling Potentials: Calculation of the Relative Free Energies and Interconversion Barriers of Glucopyranose Ring Conformers in Water
    • Hansen, H. S.; Hünenberger, P. H. Using the Local Elevation Method to Construct Optimized Umbrella Sampling Potentials: Calculation of the Relative Free Energies and Interconversion Barriers of Glucopyranose Ring Conformers in Water J. Comput. Chem. 2010, 31, 1-23 10.1002/jcc.21253
    • (2010) J. Comput. Chem. , vol.31 , pp. 1-23
    • Hansen, H.S.1    Hünenberger, P.H.2
  • 13
    • 0001616080 scopus 로고    scopus 로고
    • Replica-Exchange Molecular Dynamics Method for Protein Folding
    • Sugita, Y.; Okamoto, Y. Replica-Exchange Molecular Dynamics Method for Protein Folding Chem. Phys. Lett. 1999, 314, 141-151 10.1016/S0009-2614(99)01123-9
    • (1999) Chem. Phys. Lett. , vol.314 , pp. 141-151
    • Sugita, Y.1    Okamoto, Y.2
  • 14
    • 0035935802 scopus 로고    scopus 로고
    • Calculating Free Energies Using Average Force
    • Darve, E.; Pohorille, A. Calculating Free Energies Using Average Force J. Chem. Phys. 2001, 115, 9169-9183 10.1063/1.1410978
    • (2001) J. Chem. Phys. , vol.115 , pp. 9169-9183
    • Darve, E.1    Pohorille, A.2
  • 15
    • 84903952306 scopus 로고    scopus 로고
    • MDGRAPE-4: A Special-Purpose Computer System for Molecular Dynamics Simulations
    • Ohmura, I.; Morimoto, G.; Ohno, Y.; Hasegawa, A.; Taiji, M. MDGRAPE-4: A Special-Purpose Computer System for Molecular Dynamics Simulations Philos. Trans. R. Soc., A 2014, 372, 20130387 10.1098/rsta.2013.0387
    • (2014) Philos. Trans. R. Soc., A , vol.372 , pp. 20130387
    • Ohmura, I.1    Morimoto, G.2    Ohno, Y.3    Hasegawa, A.4    Taiji, M.5
  • 17
    • 41249087856 scopus 로고    scopus 로고
    • General Purpose Molecular Dynamics Simulations Fully Implemented on Graphics Processing Units
    • Anderson, J. A.; Lorenz, C. D.; Travesset, A. General Purpose Molecular Dynamics Simulations Fully Implemented on Graphics Processing Units J. Comput. Phys. 2008, 227, 5342-5359 10.1016/j.jcp.2008.01.047
    • (2008) J. Comput. Phys. , vol.227 , pp. 5342-5359
    • Anderson, J.A.1    Lorenz, C.D.2    Travesset, A.3
  • 18
    • 84884192184 scopus 로고    scopus 로고
    • Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUS. 2. Explicit Solvent Particle Mesh Ewald
    • Salomon-Ferrer, R.; Götz, A. W.; Poole, D.; Le Grand, S.; Walker, R. C. Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald J. Chem. Theory Comput. 2013, 9, 3878-3888 10.1021/ct400314y
    • (2013) J. Chem. Theory Comput. , vol.9 , pp. 3878-3888
    • Salomon-Ferrer, R.1    Götz, A.W.2    Poole, D.3    Le Grand, S.4    Walker, R.C.5
  • 19
    • 0016399124 scopus 로고
    • Energy Functions for Peptides and Proteins. I. Derivation of a Consistent Force Field Including the Hydrogen Bond from Amide Crystals
    • Hagler, A. T.; Huler, E.; Lifson, S. Energy Functions for Peptides and Proteins. I. Derivation of a Consistent Force Field Including the Hydrogen Bond from Amide Crystals J. Am. Chem. Soc. 1974, 96, 5319-5327 10.1021/ja00824a004
    • (1974) J. Am. Chem. Soc. , vol.96 , pp. 5319-5327
    • Hagler, A.T.1    Huler, E.2    Lifson, S.3
  • 20
    • 36849113252 scopus 로고
    • Consistent Force Field for Calculations of Conformations, Vibrational Spectra, and Enthalpies of Cycloalkane and N-Alkane Molecules
    • Lifson, S.; Warshel, A. Consistent Force Field for Calculations of Conformations, Vibrational Spectra, and Enthalpies of Cycloalkane and N-Alkane Molecules J. Chem. Phys. 1968, 49, 5116-5129 10.1063/1.1670007
    • (1968) J. Chem. Phys. , vol.49 , pp. 5116-5129
    • Lifson, S.1    Warshel, A.2
  • 21
    • 33745996625 scopus 로고
    • Calculation of Molecular Structure and Energy by Force-Field Methods
    • Allinger, N. L. Calculation of Molecular Structure and Energy by Force-Field Methods Adv. Phys. Org. Chem. 1976, 13, 1-82 10.1016/S0065-3160(08)60212-9
    • (1976) Adv. Phys. Org. Chem. , vol.13 , pp. 1-82
    • Allinger, N.L.1
  • 23
    • 33645941402 scopus 로고
    • The OPLS Potential Functions for Proteins. Energy Minimizations for Crystals of Cyclic Peptides and Crambin
    • Jorgensen, W. L.; Tirado-Rives, J. The OPLS Potential Functions for Proteins. Energy Minimizations for Crystals of Cyclic Peptides and Crambin J. Am. Chem. Soc. 1988, 110, 1657-1666 10.1021/ja00214a001
    • (1988) J. Am. Chem. Soc. , vol.110 , pp. 1657-1666
    • Jorgensen, W.L.1    Tirado-Rives, J.2
  • 25
    • 3042524904 scopus 로고
    • A Well-Behaved Electrostatic Potential Based Method Using Charge Restraints for Deriving Atomic Charges: The RESP Model
    • Bayly, C. C. I.; Cieplak, P.; Cornell, W. D.; Kollman, P. A. A Well-Behaved Electrostatic Potential Based Method Using Charge Restraints for Deriving Atomic Charges: The RESP Model J. Phys. Chem. 1993, 97, 10269-10280 10.1021/j100142a004
    • (1993) J. Phys. Chem. , vol.97 , pp. 10269-10280
    • Bayly, C.C.I.1    Cieplak, P.2    Cornell, W.D.3    Kollman, P.A.4
  • 28
    • 18744402303 scopus 로고    scopus 로고
    • Determination of Electrostatic Parameters for a Polarizable Force Field Based on the Classical Drude Oscillator
    • Anisimov, V. M.; Lamoureux, G.; Vorobyov, I. V.; Huang, N.; Roux, B.; MacKerell, A. D. Determination of Electrostatic Parameters for a Polarizable Force Field Based on the Classical Drude Oscillator J. Chem. Theory Comput. 2005, 1, 153-168 10.1021/ct049930p
    • (2005) J. Chem. Theory Comput. , vol.1 , pp. 153-168
    • Anisimov, V.M.1    Lamoureux, G.2    Vorobyov, I.V.3    Huang, N.4    Roux, B.5    MacKerell, A.D.6
  • 29
    • 36448999850 scopus 로고
    • Dynamical Fluctuating Charge Force Fields: Application to Liquid Water
    • Rick, S. W.; Stuart, S. J.; Berne, B. J. Dynamical Fluctuating Charge Force Fields: Application to Liquid Water J. Chem. Phys. 1994, 101, 6141-6156 10.1063/1.468398
    • (1994) J. Chem. Phys. , vol.101 , pp. 6141-6156
    • Rick, S.W.1    Stuart, S.J.2    Berne, B.J.3
  • 30
    • 0442311067 scopus 로고    scopus 로고
    • Development of an Accurate and Robust Polarizable Molecular Mechanics Force Field from Ab Initio Quantum Chemistry
    • Kaminski, G. A.; Stern, H. A.; Berne, B. J.; Friesner, R. A. Development of an Accurate and Robust Polarizable Molecular Mechanics Force Field from Ab Initio Quantum Chemistry J. Phys. Chem. A 2004, 108, 621-627 10.1021/jp0301103
    • (2004) J. Phys. Chem. A , vol.108 , pp. 621-627
    • Kaminski, G.A.1    Stern, H.A.2    Berne, B.J.3    Friesner, R.A.4
  • 31
    • 33645716062 scopus 로고    scopus 로고
    • Strike a Balance: Optimization of Backbone Torsion Parameters of AMBER Polarizable Force Field for Simulations of Proteins and Peptides
    • Wang, Z.-X.; Zhang, W.; Wu, C.; Lei, H.; Cieplak, P.; Duan, Y. Strike a Balance: Optimization of Backbone Torsion Parameters of AMBER Polarizable Force Field for Simulations of Proteins and Peptides J. Comput. Chem. 2006, 27, 781-790 10.1002/jcc.20386
    • (2006) J. Comput. Chem. , vol.27 , pp. 781-790
    • Wang, Z.-X.1    Zhang, W.2    Wu, C.3    Lei, H.4    Cieplak, P.5    Duan, Y.6
  • 33
    • 84890447773 scopus 로고    scopus 로고
    • Polarizable Force Field for Peptides and Proteins Based on the Classical Drude Oscillator
    • Lopes, P. E. M.; Huang, J.; Shim, J.; Luo, Y.; Li, H.; Roux, B.; Mackerell, A. D. Polarizable Force Field for Peptides and Proteins Based on the Classical Drude Oscillator J. Chem. Theory Comput. 2013, 9, 5430-5449 10.1021/ct400781b
    • (2013) J. Chem. Theory Comput. , vol.9 , pp. 5430-5449
    • Lopes, P.E.M.1    Huang, J.2    Shim, J.3    Luo, Y.4    Li, H.5    Roux, B.6    MacKerell, A.D.7
  • 34
    • 0342877286 scopus 로고
    • Determination of Partial Atomic Charges from Ab Initio Molecular Electrostatic Potentials. Application to Formamide, Methanol, and Formic Acid
    • Momany, F. A. Determination of Partial Atomic Charges from Ab Initio Molecular Electrostatic Potentials. Application to Formamide, Methanol, and Formic Acid J. Phys. Chem. 1978, 82, 592-601 10.1021/j100494a019
    • (1978) J. Phys. Chem. , vol.82 , pp. 592-601
    • Momany, F.A.1
  • 35
  • 36
    • 34548101455 scopus 로고    scopus 로고
    • Quantum Effects in Liquid Water from an Ab Initio-Based Polarizable Force Field
    • Paesani, F.; Iuchi, S.; Voth, G. A. Quantum Effects in Liquid Water from an Ab Initio-Based Polarizable Force Field J. Chem. Phys. 2007, 127, 074506 10.1063/1.2759484
    • (2007) J. Chem. Phys. , vol.127 , pp. 074506
    • Paesani, F.1    Iuchi, S.2    Voth, G.A.3
  • 37
  • 38
    • 0035976372 scopus 로고    scopus 로고
    • Derivation of Class II Force Fields. VIII. Derivation of a General Quantum Mechanical Force Field for Organic Compounds
    • Ewig, C. S.; Berry, R.; Dinur, U.; Hill, J. R.; Hwang, M. J.; Li, H.; Liang, C.; Maple, J.; Peng, Z.; Stockfisch, T. P. Derivation of Class II Force Fields. VIII. Derivation of a General Quantum Mechanical Force Field for Organic Compounds J. Comput. Chem. 2001, 22, 1782-1800 10.1002/jcc.1131
    • (2001) J. Comput. Chem. , vol.22 , pp. 1782-1800
    • Ewig, C.S.1    Berry, R.2    Dinur, U.3    Hill, J.R.4    Hwang, M.J.5    Li, H.6    Liang, C.7    Maple, J.8    Peng, Z.9    Stockfisch, T.P.10
  • 39
    • 0029912748 scopus 로고    scopus 로고
    • Development and Testing of the OLPS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids
    • Jorgensen, W. L.; Maxwell, D. S.; Tirado-Rives, J. Development and Testing of the OLPS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids J. Am. Chem. Soc. 1996, 118, 11225-11236 10.1021/ja9621760
    • (1996) J. Am. Chem. Soc. , vol.118 , pp. 11225-11236
    • Jorgensen, W.L.1    Maxwell, D.S.2    Tirado-Rives, J.3
  • 40
    • 84892596188 scopus 로고    scopus 로고
    • Optimizing Protein-Protein van der Waals Interactions for the AMBER ff9x/ff12 Force Field
    • Chapman, D. E.; Steck, J. K.; Nerenberg, P. S. Optimizing Protein-Protein van Der Waals Interactions for the AMBER ff9x/ff12 Force Field J. Chem. Theory Comput. 2014, 10, 273-281 10.1021/ct400610x
    • (2014) J. Chem. Theory Comput. , vol.10 , pp. 273-281
    • Chapman, D.E.1    Steck, J.K.2    Nerenberg, P.S.3
  • 42
    • 4444282928 scopus 로고    scopus 로고
    • A Biomolecular Force Field Based on the Free Enthalpy of Hydration and Solvation: The GROMOS Force-Field Parameter Sets 53A5 and 53A6
    • Oostenbrink, C.; Villa, A.; Mark, A. E.; Van Gunsteren, W. F. A Biomolecular Force Field Based on the Free Enthalpy of Hydration and Solvation: The GROMOS Force-Field Parameter Sets 53A5 and 53A6 J. Comput. Chem. 2004, 25, 1656-1676 10.1002/jcc.20090
    • (2004) J. Comput. Chem. , vol.25 , pp. 1656-1676
    • Oostenbrink, C.1    Villa, A.2    Mark, A.E.3    Van Gunsteren, W.F.4
  • 45
    • 3142714765 scopus 로고    scopus 로고
    • Extending the Treatment of Backbone Energetics in Protein Force Fields: Limitations of Gas-Phase Quantum Mechanics in Reproducing Protein Conformational Distributions in Molecular Dynamics Simulation
    • Mackerell, A. D.; Feig, M.; Brooks, 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 Simulation J. Comput. Chem. 2004, 25, 1400-1415 10.1002/jcc.20065
    • (2004) J. Comput. Chem. , vol.25 , pp. 1400-1415
    • MacKerell, A.D.1    Feig, M.2    Brooks, C.L.3
  • 46
    • 65249187748 scopus 로고    scopus 로고
    • Small Molecule Hydration Free Energies in Explicit Solvent: An Extensive Test of Fixed-Charge Atomistic Simulations
    • Mobley, D. L.; Bayly, C. I.; Cooper, M. D.; Shirts, M. R.; Dill, K. A. Small Molecule Hydration Free Energies in Explicit Solvent: An Extensive Test of Fixed-Charge Atomistic Simulations J. Chem. Theory Comput. 2009, 5, 350-358 10.1021/ct800409d
    • (2009) J. Chem. Theory Comput. , vol.5 , pp. 350-358
    • Mobley, D.L.1    Bayly, C.I.2    Cooper, M.D.3    Shirts, M.R.4    Dill, K.A.5
  • 47
    • 33748538013 scopus 로고    scopus 로고
    • A Kirkwood-Buff Derived Force Field for Amides
    • Kang, M.; Smith, P. E. A Kirkwood-Buff Derived Force Field for Amides J. Comput. Chem. 2006, 27, 1477-1485 10.1002/jcc.20441
    • (2006) J. Comput. Chem. , vol.27 , pp. 1477-1485
    • Kang, M.1    Smith, P.E.2
  • 48
    • 0038203549 scopus 로고    scopus 로고
    • Kirkwood-Buff Derived Force Field for Mixtures of Acetone and Water
    • Weerasinghe, S.; Smith, P. E. Kirkwood-Buff Derived Force Field for Mixtures of Acetone and Water J. Chem. Phys. 2003, 118, 10663 10.1063/1.1574773
    • (2003) J. Chem. Phys. , vol.118 , pp. 10663
    • Weerasinghe, S.1    Smith, P.E.2
  • 50
    • 2942622288 scopus 로고    scopus 로고
    • Development of an Improved Four-Site Water Model for Biomolecular Simulations: TIP4P-Ew
    • Horn, H. W.; Swope, W. C.; Pitera, J. W.; Madura, J. D.; Dick, T. J.; Hura, G. L.; Head-Gordon, T. Development of an Improved Four-Site Water Model for Biomolecular Simulations: TIP4P-Ew J. Chem. Phys. 2004, 120, 9665-9678 10.1063/1.1683075
    • (2004) J. Chem. Phys. , vol.120 , pp. 9665-9678
    • Horn, H.W.1    Swope, W.C.2    Pitera, J.W.3    Madura, J.D.4    Dick, T.J.5    Hura, G.L.6    Head-Gordon, T.7
  • 51
    • 24144479792 scopus 로고    scopus 로고
    • Solvation Free Energies of Amino Acid Side Chain Analogs for Common Molecular Mechanics Water Models
    • Shirts, M. R.; Pande, V. S. Solvation Free Energies of Amino Acid Side Chain Analogs for Common Molecular Mechanics Water Models J. Chem. Phys. 2005, 122, 134508 10.1063/1.1877132
    • (2005) J. Chem. Phys. , vol.122 , pp. 134508
    • Shirts, M.R.1    Pande, V.S.2
  • 52
    • 33947397110 scopus 로고    scopus 로고
    • Comparison of Charge Models for Fixed-Charge Force Fields: Small-Molecule Hydration Free Energies in Explicit Solvent
    • Mobley, D. L.; Dumont, é.; Chodera, J. D.; Dill, K. A. Comparison of Charge Models for Fixed-Charge Force Fields: Small-Molecule Hydration Free Energies in Explicit Solvent J. Phys. Chem. B 2007, 111, 2242-2254 10.1021/jp0667442
    • (2007) J. Phys. Chem. B , vol.111 , pp. 2242-2254
    • Mobley, D.L.1    Chodera, J.D.2    Dill, K.A.3
  • 53
    • 84907168646 scopus 로고    scopus 로고
    • Bridging Calorimetry and Simulation through Precise Calculations of Cucurbituril - Guest Binding Enthalpies
    • Fenley, A. T.; Henriksen, N. M.; Muddana, H. S.; Gilson, M. K. Bridging Calorimetry and Simulation through Precise Calculations of Cucurbituril-Guest Binding Enthalpies J. Chem. Theory Comput. 2014, 10, 4069-4078 10.1021/ct5004109
    • (2014) J. Chem. Theory Comput. , vol.10 , pp. 4069-4078
    • Fenley, A.T.1    Henriksen, N.M.2    Muddana, H.S.3    Gilson, M.K.4
  • 54
    • 4143081344 scopus 로고    scopus 로고
    • Simple, Intuitive Calculations of Free Energy of Binding for Protein-Ligand Complexes. 3. the Free Energy Contribution of Structural Water Molecules in HIV-1 Protease Complexes
    • Fornabaio, M.; Spyrakis, F.; Mozzarelli, A.; Cozzini, P.; Abraham, D. J.; Kellogg, G. E. Simple, Intuitive Calculations of Free Energy of Binding for Protein-Ligand Complexes. 3. The Free Energy Contribution of Structural Water Molecules in HIV-1 Protease Complexes J. Med. Chem. 2004, 47, 4507-4516 10.1021/jm030596b
    • (2004) J. Med. Chem. , vol.47 , pp. 4507-4516
    • Fornabaio, M.1    Spyrakis, F.2    Mozzarelli, A.3    Cozzini, P.4    Abraham, D.J.5    Kellogg, G.E.6
  • 55
    • 0032961895 scopus 로고    scopus 로고
    • The Particle Concept: Placing Discrete Water Molecules during Protein- Ligand Docking Predictions
    • Rarey, M.; Kramer, B.; Lengauer, T. The Particle Concept: Placing Discrete Water Molecules during Protein- Ligand Docking Predictions Proteins: Struct., Funct., Genet. 1999, 34, 17-28 10.1002/(SICI)1097-0134(19990101)34:1<17::AID-PROT3>3.3.CO;2-T
    • (1999) Proteins: Struct., Funct., Genet. , vol.34 , pp. 17-28
    • Rarey, M.1    Kramer, B.2    Lengauer, T.3
  • 56
    • 2942659093 scopus 로고    scopus 로고
    • Standard Free Energy of Releasing a Localized Water Molecule from the Binding Pockets of Proteins: Double-Decoupling Method
    • Hamelberg, D.; McCammon, J. A. Standard Free Energy of Releasing a Localized Water Molecule from the Binding Pockets of Proteins: Double-Decoupling Method J. Am. Chem. Soc. 2004, 126, 7683-7689 10.1021/ja0377908
    • (2004) J. Am. Chem. Soc. , vol.126 , pp. 7683-7689
    • Hamelberg, D.1    McCammon, J.A.2
  • 57
    • 33748513468 scopus 로고    scopus 로고
    • Binding Free Energy Contributions of Interfacial Waters in HIV-1 Protease/inhibitor Complexes
    • Lu, Y.; Yang, C. Y.; Wang, S. Binding Free Energy Contributions of Interfacial Waters in HIV-1 Protease/inhibitor Complexes J. Am. Chem. Soc. 2006, 128, 11830-11839 10.1021/ja058042g
    • (2006) J. Am. Chem. Soc. , vol.128 , pp. 11830-11839
    • Lu, Y.1    Yang, C.Y.2    Wang, S.3
  • 58
    • 33846524439 scopus 로고    scopus 로고
    • Motifs for molecular recognition exploiting hydrophobic enclosure in protein-ligand binding
    • Young, T.; Abel, R.; Kim, B.; Berne, B. J.; Friesner, R. A. Motifs for molecular recognition exploiting hydrophobic enclosure in protein-ligand binding Proc. Natl. Acad. Sci. U. S. A. 2007, 104, 808-813 10.1073/pnas.0610202104
    • (2007) Proc. Natl. Acad. Sci. U. S. A. , vol.104 , pp. 808-813
    • Young, T.1    Abel, R.2    Kim, B.3    Berne, B.J.4    Friesner, R.A.5
  • 59
    • 84988603747 scopus 로고    scopus 로고
    • Grid inhomogeneous solvation theory: Hydration structure and thermodynamics of the miniature receptor cucurbit[7]uril
    • Nguyen, C. N.; Kurtzman Young, T.; Gilson, M. K. Grid inhomogeneous solvation theory: Hydration structure and thermodynamics of the miniature receptor cucurbit[7]uril J. Chem. Phys. 2012, 137, 044101 10.1063/1.4733951
    • (2012) J. Chem. Phys. , vol.137 , pp. 044101
    • Nguyen, C.N.1    Kurtzman Young, T.2    Gilson, M.K.3
  • 61
    • 5644287368 scopus 로고    scopus 로고
    • Free Energy, Entropy, and Induced Fit in Host-Guest Recognition: Calculations with the Second-Generation Mining Minima Algorithm
    • Chang, C.; Gilson, M. K. Free Energy, Entropy, and Induced Fit in Host-Guest Recognition: Calculations with the Second-Generation Mining Minima Algorithm J. Am. Chem. Soc. 2004, 126, 13156-13164 10.1021/ja047115d
    • (2004) J. Am. Chem. Soc. , vol.126 , pp. 13156-13164
    • Chang, C.1    Gilson, M.K.2
  • 62
    • 79952586541 scopus 로고    scopus 로고
    • New Ultrahigh Affinity Host - Guest Complexes of Cucurbit [ 7 ] Uril with Bicyclo [ 2. 2. 2 ] Octane and Adamantane Guests: Thermodynamic Analysis and Evaluation of M2 Affinity Calculations
    • Moghaddam, S.; Yang, C.; Rekharsky, M.; Ko, Y. H.; Kim, K.; Inoue, Y.; Gilson, M. K. New Ultrahigh Affinity Host-Guest Complexes of Cucurbit [ 7 ] Uril with Bicyclo [ 2. 2. 2 ] Octane and Adamantane Guests: Thermodynamic Analysis and Evaluation of M2 Affinity Calculations J. Am. Chem. Soc. 2011, 133, 3570-3581 10.1021/ja109904u
    • (2011) J. Am. Chem. Soc. , vol.133 , pp. 3570-3581
    • Moghaddam, S.1    Yang, C.2    Rekharsky, M.3    Ko, Y.H.4    Kim, K.5    Inoue, Y.6    Gilson, M.K.7
  • 63
    • 67849083399 scopus 로고    scopus 로고
    • Host-Guest Complexes with Protein-Ligand-like Affinities: Computational Analysis and Design
    • Moghaddam, S.; Inoue, Y.; Gilson, M. K. Host-Guest Complexes with Protein-Ligand-like Affinities: Computational Analysis and Design J. Am. Chem. Soc. 2009, 131, 4012-4021 10.1021/ja808175m
    • (2009) J. Am. Chem. Soc. , vol.131 , pp. 4012-4021
    • Moghaddam, S.1    Inoue, Y.2    Gilson, M.K.3
  • 66
  • 67
    • 84880029510 scopus 로고    scopus 로고
    • Large Scale Affinity Calculations of Cyclodextrin Host-Guest Complexes: Understanding the Role of Reorganization in the Molecular Recognition Process
    • Wickstrom, L.; He, P.; Gallicchio, E.; Levy, R. M. Large Scale Affinity Calculations of Cyclodextrin Host-Guest Complexes: Understanding the Role of Reorganization in the Molecular Recognition Process J. Chem. Theory Comput. 2013, 9, 3136-3150 10.1021/ct400003r
    • (2013) J. Chem. Theory Comput. , vol.9 , pp. 3136-3150
    • Wickstrom, L.1    He, P.2    Gallicchio, E.3    Levy, R.M.4
  • 68
    • 0000223084 scopus 로고
    • Thermodynamics of Molecular Recognition by Cyclodextrins 1. Calorimetric Titration of Inclusion Complexation of Naphthalenesulfonates with a-, B-, and G-Cyclodextrins: Enthalpy-Entropy Compensation
    • Inoue, Y.; Hakushi, T.; Liu, Y.; Tong, L.-H.; Shen, B.-J.; Jin, D.-S. Thermodynamics of Molecular Recognition by Cyclodextrins 1. Calorimetric Titration of Inclusion Complexation of Naphthalenesulfonates with a-, B-, and G-Cyclodextrins: Enthalpy-Entropy Compensation J. Am. Chem. Soc. 1993, 115, 475-481 10.1021/ja00055a017
    • (1993) J. Am. Chem. Soc. , vol.115 , pp. 475-481
    • Inoue, Y.1    Hakushi, T.2    Liu, Y.3    Tong, L.-H.4    Shen, B.-J.5    Jin, D.-S.6
  • 69
    • 0034630938 scopus 로고    scopus 로고
    • Chiral Recognition Thermodynamics of Beta-Cyclodextrin: The Thermodynamic Origin of Enantioselectivity and the Enthalpa-Entropy Compensation Effect
    • Rekharsky, M.; Inoue, Y. Chiral Recognition Thermodynamics of Beta-Cyclodextrin: The Thermodynamic Origin of Enantioselectivity and the Enthalpa-Entropy Compensation Effect J. Am. Chem. Soc. 2000, 122, 4418-4435 10.1021/ja9921118
    • (2000) J. Am. Chem. Soc. , vol.122 , pp. 4418-4435
    • Rekharsky, M.1    Inoue, Y.2
  • 70
    • 84866489777 scopus 로고    scopus 로고
    • Binding Free Energy, Energy and Entropy Calculations Using Simple Model Systems
    • Lai, B.; Oostenbrink, C. Binding Free Energy, Energy and Entropy Calculations Using Simple Model Systems Theor. Chem. Acc. 2012, 131, 1272 10.1007/s00214-012-1272-1
    • (2012) Theor. Chem. Acc. , vol.131 , pp. 1272
    • Lai, B.1    Oostenbrink, C.2
  • 71
    • 0030474049 scopus 로고    scopus 로고
    • What Can We Learn from Molecular Recognition in Protein-Ligand Complexes for the Design of New Drugs?
    • Bohm, H.; Klebe, G. What Can We Learn from Molecular Recognition in Protein-Ligand Complexes for the Design of New Drugs? Angew. Chem., Int. Ed. Engl. 1996, 35, 2588-2614 10.1002/anie.199625881
    • (1996) Angew. Chem., Int. Ed. Engl. , vol.35 , pp. 2588-2614
    • Bohm, H.1    Klebe, G.2
  • 72
    • 76249087938 scopus 로고    scopus 로고
    • CHARMM General Force Field: A Force Field for Drug-like Molecules Compatible with the CHARMM All-Atom Additive Biological Force Fields
    • Vanommeslaeghe, K.; Hatcher, E.; Acharya, C.; Kundu, S.; Zhong, S.; Shim, J.; Darian, E.; Guvench, O.; Lopes, P.; Vorobyov, I. CHARMM General Force Field: A Force Field for Drug-like Molecules Compatible with the CHARMM All-Atom Additive Biological Force Fields J. Comput. Chem. 2010, 31, 671-690 10.1002/jcc.21367
    • (2010) J. Comput. Chem. , vol.31 , pp. 671-690
    • Vanommeslaeghe, K.1    Hatcher, E.2    Acharya, C.3    Kundu, S.4    Zhong, S.5    Shim, J.6    Darian, E.7    Guvench, O.8    Lopes, P.9    Vorobyov, I.10
  • 73
    • 0029912748 scopus 로고    scopus 로고
    • Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids
    • Jorgensen, W. L.; Maxwell, D. S.; Tirado-Rives, J. Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids J. Am. Chem. Soc. 1996, 118, 11225-11236 10.1021/ja9621760
    • (1996) J. Am. Chem. Soc. , vol.118 , pp. 11225-11236
    • Jorgensen, W.L.1    Maxwell, D.S.2    Tirado-Rives, J.3
  • 74
    • 84855671158 scopus 로고    scopus 로고
    • Force Field Benchmark of Organic Liquids: Density, Enthalpy of Vaporization, Heat Capacities, Surface Tension, Isothermal Compressibility, Volumetric Expansion Coefficient, and Dielectric Constant
    • Caleman, C.; Van Maaren, P. J.; Hong, M.; Hub, J. S.; Costa, L. T.; Van Der Spoel, D. Force Field Benchmark of Organic Liquids: Density, Enthalpy of Vaporization, Heat Capacities, Surface Tension, Isothermal Compressibility, Volumetric Expansion Coefficient, and Dielectric Constant J. Chem. Theory Comput. 2012, 8, 61-74 10.1021/ct200731v
    • (2012) J. Chem. Theory Comput. , vol.8 , pp. 61-74
    • Caleman, C.1    Van Maaren, P.J.2    Hong, M.3    Hub, J.S.4    Costa, L.T.5    Van Der Spoel, D.6
  • 76
    • 84921482880 scopus 로고    scopus 로고
    • Optimizing Potentials for a Liquid Mixture: A New Force Field for a Tert-Butanol and Water Solution
    • Di Pierro, M.; Mugnai, M. L.; Elber, R. Optimizing Potentials for a Liquid Mixture: A New Force Field for a Tert-Butanol and Water Solution J. Phys. Chem. B 2015, 119, 836 10.1021/jp505401m
    • (2015) J. Phys. Chem. B , vol.119 , pp. 836
    • Di Pierro, M.1    Mugnai, M.L.2    Elber, R.3
  • 77
    • 84882304520 scopus 로고    scopus 로고
    • Automated Optimization of Potential Parameters
    • Di Pierro, M.; Elber, R. Automated Optimization of Potential Parameters J. Chem. Theory Comput. 2013, 9, 3311-3320 10.1021/ct400313n
    • (2013) J. Chem. Theory Comput. , vol.9 , pp. 3311-3320
    • Di Pierro, M.1    Elber, R.2
  • 78
    • 84902079388 scopus 로고    scopus 로고
    • Building Force Fields: An Automatic, Systematic, and Reproducible Approach
    • Wang, L. P.; Martinez, T. J.; Pande, V. S. Building Force Fields: An Automatic, Systematic, and Reproducible Approach J. Phys. Chem. Lett. 2014, 5, 1885-1891 10.1021/jz500737m
    • (2014) J. Phys. Chem. Lett. , vol.5 , pp. 1885-1891
    • Wang, L.P.1    Martinez, T.J.2    Pande, V.S.3
  • 80
    • 54949109484 scopus 로고    scopus 로고
    • The Relative Entropy Is Fundamental to Multiscale and Inverse Thermodynamic Problems
    • Shell, M. S. The Relative Entropy Is Fundamental to Multiscale and Inverse Thermodynamic Problems J. Chem. Phys. 2008, 129, 144108 10.1063/1.2992060
    • (2008) J. Chem. Phys. , vol.129 , pp. 144108
    • Shell, M.S.1
  • 82
    • 0041472445 scopus 로고    scopus 로고
    • Cucurbituril Homologues and Derivatives: New Opportunities in Supramolecular Chemistry
    • Lee, J. W.; Samal, S.; Selvapalam, N.; Kim, H.-J.; Kim, K. Cucurbituril Homologues and Derivatives: New Opportunities in Supramolecular Chemistry Acc. Chem. Res. 2003, 36, 621-630 10.1021/ar020254k
    • (2003) Acc. Chem. Res. , vol.36 , pp. 621-630
    • Lee, J.W.1    Samal, S.2    Selvapalam, N.3    Kim, H.-J.4    Kim, K.5
  • 84
    • 20844431667 scopus 로고    scopus 로고
    • Novel Molecular Drug Carrier: Encapsulation of Oxaliplatin in cucurbit[7]uril and Its Effects on Stability and Reactivity of the Drug
    • Jeon, Y. J.; Kim, S.-Y.; Ko, Y. H.; Sakamoto, S.; Yamaguchi, K.; Kim, K. Novel Molecular Drug Carrier: Encapsulation of Oxaliplatin in cucurbit[7]uril and Its Effects on Stability and Reactivity of the Drug Org. Biomol. Chem. 2005, 3, 2122-2125 10.1039/b504487a
    • (2005) Org. Biomol. Chem. , vol.3 , pp. 2122-2125
    • Jeon, Y.J.1    Kim, S.-Y.2    Ko, Y.H.3    Sakamoto, S.4    Yamaguchi, K.5    Kim, K.6
  • 85
    • 84884902749 scopus 로고    scopus 로고
    • Overcoming Dissipation in the Calculation of Standard Binding Free Energies by Ligand Extraction
    • Velez-Vega, C.; Gilson, M. K. Overcoming Dissipation in the Calculation of Standard Binding Free Energies by Ligand Extraction J. Comput. Chem. 2013, 34, 2360-2371 10.1002/jcc.23398
    • (2013) J. Comput. Chem. , vol.34 , pp. 2360-2371
    • Velez-Vega, C.1    Gilson, M.K.2
  • 86
    • 36849122972 scopus 로고
    • High-Temperature Equation of State by a Perturbation Method. I. Nonpolar Gases
    • Zwanzig, R. High-Temperature Equation of State by a Perturbation Method. I. Nonpolar Gases J. Chem. Phys. 1954, 22, 1420-1426 10.1063/1.1740409
    • (1954) J. Chem. Phys. , vol.22 , pp. 1420-1426
    • Zwanzig, R.1
  • 87
    • 33646471468 scopus 로고
    • Statistical Mechanics of Fluid Mixtures
    • Kirkwood, J. G. Statistical Mechanics of Fluid Mixtures J. Chem. Phys. 1935, 3, 300-313 10.1063/1.1749657
    • (1935) J. Chem. Phys. , vol.3 , pp. 300-313
    • Kirkwood, J.G.1
  • 88
    • 0342929614 scopus 로고
    • Nonphysical Sampling Distributions in Monte Carlo Free-Energy Estimation: Umbrella Sampling
    • Torrie, G. M.; Valleau, J. P. Nonphysical Sampling Distributions in Monte Carlo Free-Energy Estimation: Umbrella Sampling J. Comput. Phys. 1977, 23, 187-199 10.1016/0021-9991(77)90121-8
    • (1977) J. Comput. Phys. , vol.23 , pp. 187-199
    • Torrie, G.M.1    Valleau, J.P.2
  • 90
    • 0001041959 scopus 로고    scopus 로고
    • Fast, Efficient Generation of High-Quality Atomic Charges. AM1-BCC Model: I. Method
    • Jakalian, A.; Bush, B. L.; Jack, D. B.; Bayly, C. I. Fast, Efficient Generation of High-Quality Atomic Charges. AM1-BCC Model: I. Method J. Comput. Chem. 2000, 21, 132-146 10.1002/(SICI)1096-987X(20000130)21:2<132::AID-JCC5>3.0.CO;2-P
    • (2000) J. Comput. Chem. , vol.21 , pp. 132-146
    • Jakalian, A.1    Bush, B.L.2    Jack, D.B.3    Bayly, C.I.4
  • 91
    • 0036890178 scopus 로고    scopus 로고
    • Fast, Efficient Generation of High-Quality Atomic Charges. AM1-BCC Model: II. Parameterization and Validation
    • Jakalian, A.; Jack, D. B.; Bayly, C. I. Fast, Efficient Generation of High-Quality Atomic Charges. AM1-BCC Model: II. Parameterization and Validation J. Comput. Chem. 2002, 23, 1623-1641 10.1002/jcc.10128
    • (2002) J. Comput. Chem. , vol.23 , pp. 1623-1641
    • Jakalian, A.1    Jack, D.B.2    Bayly, C.I.3
  • 92
    • 33748538349 scopus 로고    scopus 로고
    • Automatic Atom Type and Bond Type Perception in Molecular Mechanical Calculations
    • Wang, J.; Wang, W.; Kollman, P. A.; Case, D. A. Automatic Atom Type and Bond Type Perception in Molecular Mechanical Calculations J. Mol. Graphics Modell. 2006, 25, 247-260 10.1016/j.jmgm.2005.12.005
    • (2006) J. Mol. Graphics Modell. , vol.25 , pp. 247-260
    • Wang, J.1    Wang, W.2    Kollman, P.A.3    Case, D.A.4
  • 93
    • 36549102647 scopus 로고
    • Error Estimates on Averages of Correlated Data
    • Flyvbjerg, H.; Petersen, H. G. Error Estimates on Averages of Correlated Data J. Chem. Phys. 1989, 91, 461-466 10.1063/1.457480
    • (1989) J. Chem. Phys. , vol.91 , pp. 461-466
    • Flyvbjerg, H.1    Petersen, H.G.2
  • 94
    • 18844402460 scopus 로고
    • Nonlinear Generalized Langevin Equations
    • Zwanzig, R. Nonlinear Generalized Langevin Equations J. Stat. Phys. 1973, 9, 215-220 10.1007/BF01008729
    • (1973) J. Stat. Phys. , vol.9 , pp. 215-220
    • Zwanzig, R.1
  • 96
    • 33846823909 scopus 로고
    • Particle Mesh Ewald: An N log(N) Method for Ewald Sums in Large Systems
    • Darden, T.; York, D.; Pedersen, L. Particle Mesh Ewald: An N log(N) Method for Ewald Sums in Large Systems J. Chem. Phys. 1993, 98, 10089 10.1063/1.464397
    • (1993) J. Chem. Phys. , vol.98 , pp. 10089
    • Darden, T.1    York, D.2    Pedersen, L.3
  • 97
    • 65249112693 scopus 로고    scopus 로고
    • Predictions of Hydration Free Energies from All-Atom Molecular Dynamics Simulations
    • Mobley, D. L.; Bayly, C. I.; Cooper, M. D.; Dill, K. A. Predictions of Hydration Free Energies from All-Atom Molecular Dynamics Simulations J. Phys. Chem. B 2009, 113, 4533-4537 10.1021/jp806838b
    • (2009) J. Phys. Chem. B , vol.113 , pp. 4533-4537
    • Mobley, D.L.1    Bayly, C.I.2    Cooper, M.D.3    Dill, K.A.4
  • 99
    • 4243778369 scopus 로고    scopus 로고
    • Complexation Thermodynamics of Cyclodextrins
    • Rekharsky, M. V.; Inoue, Y. Complexation Thermodynamics of Cyclodextrins Chem. Rev. 1998, 98, 1875-1918 10.1021/cr970015o
    • (1998) Chem. Rev. , vol.98 , pp. 1875-1918
    • Rekharsky, M.V.1    Inoue, Y.2
  • 100
    • 33845281571 scopus 로고
    • Rigid Molecular Tweezers: Synthesis, Characterization, and Complexation Chemistry of a Diacridine
    • Zimmerman, S. C.; Vanzyl, C. M. Rigid Molecular Tweezers: Synthesis, Characterization, and Complexation Chemistry of a Diacridine J. Am. Chem. Soc. 1987, 109, 7894-7896 10.1021/ja00259a055
    • (1987) J. Am. Chem. Soc. , vol.109 , pp. 7894-7896
    • Zimmerman, S.C.1    Vanzyl, C.M.2
  • 101
    • 0002344388 scopus 로고
    • Rigid Molecular Tweezers as Hosts for the Complexation of Neutral Guests
    • Topics in Current Chemistry; Springer: Berlin
    • Zimmerman, S. C. Rigid Molecular Tweezers as Hosts for the Complexation of Neutral Guests. In Supramolecular Chemistry I-Directed Synthesis and Molecular Recognition; Weber, E., Ed.; Topics in Current Chemistry 165; Springer: Berlin, 1993; pp 71-102.
    • (1993) Supramolecular Chemistry I-Directed Synthesis and Molecular Recognition , vol.165 , pp. 71-102
    • Zimmerman, S.C.1    Weber, E.2
  • 102
    • 17944388214 scopus 로고    scopus 로고
    • Molecular Tweezers and Clips as Synthetic Receptors. Molecular Recognition and Dynamics in Receptor-Substrate Complexes
    • Klärner, F. G.; Kahlert, B. Molecular Tweezers and Clips as Synthetic Receptors. Molecular Recognition and Dynamics in Receptor-Substrate Complexes Acc. Chem. Res. 2003, 36, 919-932 10.1021/ar0200448
    • (2003) Acc. Chem. Res. , vol.36 , pp. 919-932
    • Klärner, F.G.1    Kahlert, B.2
  • 104
    • 0033153544 scopus 로고    scopus 로고
    • Host-Guest Chemistry: Combinatorial Receptors
    • Linton, B.; Hamilton, A. D. Host-Guest Chemistry: Combinatorial Receptors Curr. Opin. Chem. Biol. 1999, 3, 307-312 10.1016/S1367-5931(99)80047-7
    • (1999) Curr. Opin. Chem. Biol. , vol.3 , pp. 307-312
    • Linton, B.1    Hamilton, A.D.2
  • 105
    • 0017305059 scopus 로고
    • Total Chromatographic Optical Resolutions Of. Alpha.-Amino Acid and Ester Salts through Chiral Recognition by a Host Covalently Bound to Polystyrene Resin
    • Dotsevi, G.; Sogah, Y.; Cram, D. J. Total Chromatographic Optical Resolutions Of. Alpha.-Amino Acid and Ester Salts through Chiral Recognition by a Host Covalently Bound to Polystyrene Resin J. Am. Chem. Soc. 1976, 98, 3038-3041 10.1021/ja00426a073
    • (1976) J. Am. Chem. Soc. , vol.98 , pp. 3038-3041
    • Dotsevi, G.1    Sogah, Y.2    Cram, D.J.3
  • 106
    • 33947092416 scopus 로고
    • Host-Guest Complexation. 8. Macrocyclic Polyethers Shaped by Two Rigid Substituted Dinaphthyl or Ditetralyl Units
    • Cram, D.; Helgeson, R. Host-Guest Complexation. 8. Macrocyclic Polyethers Shaped by Two Rigid Substituted Dinaphthyl or Ditetralyl Units J. Org. Chem. 1978, 43, 1930-1946 10.1021/jo00404a019
    • (1978) J. Org. Chem. , vol.43 , pp. 1930-1946
    • Cram, D.1    Helgeson, R.2
  • 107
    • 0034696923 scopus 로고    scopus 로고
    • Host-guest Chemistry of Calixarene Capsules
    • Rebek, J., Jr. Host-guest Chemistry of Calixarene Capsules Chem. Commun. 2000, 637-643 10.1039/a910339m
    • (2000) Chem. Commun. , pp. 637-643
    • Rebek, J.1
  • 108
    • 0001253745 scopus 로고
    • Molecular Recognition: Ionic and Aromatic Stacking Interactions Bind Complementary Functional Groups in a Molecular Cleft
    • Rebek, J., Jr.; Nemeth, D. Molecular Recognition: Ionic and Aromatic Stacking Interactions Bind Complementary Functional Groups in a Molecular Cleft J. Am. Chem. Soc. 1986, 108, 5637-5638 10.1021/ja00278a052
    • (1986) J. Am. Chem. Soc. , vol.108 , pp. 5637-5638
    • Rebek, J.1    Nemeth, D.2
  • 109
    • 84988062551 scopus 로고
    • Progress in Molecular Recognition
    • Liebman, J. F. Greenberg, A. VCH Publishers: New York
    • Rebek, J., Jr. Progress in Molecular Recognition. In Environmental Influences and Recognition in Enzyme Chemistry; Liebman, J. F.; Greenberg, A., Eds.; VCH Publishers: New York, 1988; pp 291-250.
    • (1988) Environmental Influences and Recognition in Enzyme Chemistry , pp. 291-350
    • Rebek, J.1
  • 110
    • 0025989335 scopus 로고
    • Hydrogen Bonding and Molecular Recognition: Synthetic, Complexation, Amd Structural Studies on Barbiturate Binding to an Artificial Receptor
    • Chang, S. K.; van Engen, D.; Fan, E.; Hamilton, A. D. Hydrogen Bonding and Molecular Recognition: Synthetic, Complexation, Amd Structural Studies on Barbiturate Binding to an Artificial Receptor J. Am. Chem. Soc. 1991, 113, 7640-7645 10.1021/ja00020a027
    • (1991) J. Am. Chem. Soc. , vol.113 , pp. 7640-7645
    • Chang, S.K.1    Van Engen, D.2    Fan, E.3    Hamilton, A.D.4
  • 111
    • 84877768087 scopus 로고    scopus 로고
    • Entropy-Enthalpy Compensation: Role and Ramifications in Biomolecular Ligand Recognition and Design
    • Chodera, J. D.; Mobley, D. L. Entropy-Enthalpy Compensation: Role and Ramifications in Biomolecular Ligand Recognition and Design Annu. Rev. Biophys. 2013, 42, 121-142 10.1146/annurev-biophys-083012-130318
    • (2013) Annu. Rev. Biophys. , vol.42 , pp. 121-142
    • Chodera, J.D.1    Mobley, D.L.2
  • 112
    • 0035107447 scopus 로고    scopus 로고
    • Entropy-Enthalpy Compensation: Fact or Artifact?
    • Sharp, K. Entropy-Enthalpy Compensation: Fact or Artifact? Protein Sci. 2001, 10, 661-667 10.1110/ps.37801
    • (2001) Protein Sci. , vol.10 , pp. 661-667
    • Sharp, K.1
  • 113
    • 84870579518 scopus 로고    scopus 로고
    • Entropy-Enthalpy Transduction Caused by Conformational Shifts Can Obscure the Forces Driving Protein-Ligand Binding
    • Fenley, A. T.; Muddana, H. S.; Gilson, M. K. Entropy-Enthalpy Transduction Caused by Conformational Shifts Can Obscure the Forces Driving Protein-Ligand Binding Proc. Natl. Acad. Sci. U. S. A. 2012, 109, 20006-20011 10.1073/pnas.1213180109
    • (2012) Proc. Natl. Acad. Sci. U. S. A. , vol.109 , pp. 20006-20011
    • Fenley, A.T.1    Muddana, H.S.2    Gilson, M.K.3
  • 114
    • 0014722597 scopus 로고
    • Enthalpy-Entropy Compensation Phenomena in Water Solutions of Proteins and Small Molecules: A Ubiquitous Property of Water
    • Lumry, R.; Rajender, S. Enthalpy-Entropy Compensation Phenomena in Water Solutions of Proteins and Small Molecules: A Ubiquitous Property of Water Biopolymers 1970, 9, 1125-1227 10.1002/bip.1970.360091002
    • (1970) Biopolymers , vol.9 , pp. 1125-1227
    • Lumry, R.1    Rajender, S.2
  • 115
    • 0029395478 scopus 로고
    • Win Some, Lose Some: Enthalpy-Entropy Compensation in Weak Intermolecular Interactions
    • Dunitz, J. D. Win Some, Lose Some: Enthalpy-Entropy Compensation in Weak Intermolecular Interactions Chem. Biol. 1995, 2, 709-712 10.1016/1074-5521(95)90097-7
    • (1995) Chem. Biol. , vol.2 , pp. 709-712
    • Dunitz, J.D.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.