메뉴 건너뛰기




Volumn 10, Issue 9, 2014, Pages 4069-4078

Bridging calorimetry and simulation through precise calculations of cucurbituril-guest binding enthalpies

Author keywords

[No Author keywords available]

Indexed keywords


EID: 84907168646     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/ct5004109     Document Type: Article
Times cited : (87)

References (81)
  • 1
    • 0024356301 scopus 로고
    • Rapid Measurement of Binding Constants and Heats of Binding Using a New Titration Calorimeter
    • Wiseman, T.; Williston, S.; Brandts, J. F.; Lin, L.-N. Rapid Measurement of Binding Constants and Heats of Binding Using a New Titration Calorimeter Anal. Biochem. 1989, 179, 131-137
    • (1989) Anal. Biochem. , vol.179 , pp. 131-137
    • Wiseman, T.1    Williston, S.2    Brandts, J.F.3    Lin, L.-N.4
  • 2
    • 0041854716 scopus 로고    scopus 로고
    • Understanding Binding Affinity: A Combined Isothermal Titration Calorimetry/Molecular Dynamics Study of the Binding of a Series of Hydrophobically Modified Benzamidinium Chloride Inhibitors to Trypsin
    • Talhout, R.; Villa, A.; Mark, A. E.; Engberts, J. B. F. N. Understanding Binding Affinity: A Combined Isothermal Titration Calorimetry/Molecular Dynamics Study of the Binding of a Series of Hydrophobically Modified Benzamidinium Chloride Inhibitors to Trypsin J. Am. Chem. Soc. 2003, 125, 10570-10579
    • (2003) J. Am. Chem. Soc. , vol.125 , pp. 10570-10579
    • Talhout, R.1    Villa, A.2    Mark, A.E.3    Engberts, J.B.F.N.4
  • 3
    • 77953631827 scopus 로고    scopus 로고
    • A Medicinal Chemist's Guide to Molecular Interactions
    • Bissantz, C.; Kuhn, B.; Stahl, M. A Medicinal Chemist's Guide to Molecular Interactions J. Med. Chem. 2010, 53, 5061-5084
    • (2010) J. Med. Chem. , vol.53 , pp. 5061-5084
    • Bissantz, C.1    Kuhn, B.2    Stahl, M.3
  • 4
    • 79959243001 scopus 로고    scopus 로고
    • Thermodynamics of Ligand Binding and Efficiency
    • Reynolds, C. H.; Holloway, M. K. Thermodynamics of Ligand Binding and Efficiency ACS Med. Chem. Lett. 2011, 2, 433-437
    • (2011) ACS Med. Chem. Lett. , vol.2 , pp. 433-437
    • Reynolds, C.H.1    Holloway, M.K.2
  • 5
    • 14744271960 scopus 로고    scopus 로고
    • ITC in the Post-Genomic Era? Priceless
    • Velázquez Campoy, A.; Freire, E. ITC in the Post-Genomic Era? Priceless Biophys. Chem. 2005, 115, 115-124
    • (2005) Biophys. Chem. , vol.115 , pp. 115-124
    • Velázquez Campoy, A.1    Freire, E.2
  • 6
    • 52049123291 scopus 로고    scopus 로고
    • Do Enthalpy and Entropy Distinguish First in Class from Best in Class?
    • Freire, E. Do Enthalpy and Entropy Distinguish First in Class from Best in Class? Drug Discovery Today 2008, 13, 869-874
    • (2008) Drug Discovery Today , vol.13 , pp. 869-874
    • Freire, E.1
  • 7
    • 74149083849 scopus 로고    scopus 로고
    • Adding Calorimetric Data to Decision Making in Lead Discovery: A Hot Tip
    • Ladbury, J. E.; Klebe, G.; Freire, E. Adding Calorimetric Data to Decision Making in Lead Discovery: A Hot Tip Nat. Rev. Drug Discovery 2010, 9, 23-27
    • (2010) Nat. Rev. Drug Discovery , vol.9 , pp. 23-27
    • Ladbury, J.E.1    Klebe, G.2    Freire, E.3
  • 8
    • 0014722597 scopus 로고
    • Enthalpy-Entropy Compensation Phenomena in Water Solutions of Proteins and Small Molecules: A Ubiquitous Properly of Water
    • Lumry, R.; Rajender, S. Enthalpy-Entropy Compensation Phenomena in Water Solutions of Proteins and Small Molecules: A Ubiquitous Properly of Water Biopolymers 1970, 9, 1125-1227
    • (1970) Biopolymers , vol.9 , pp. 1125-1227
    • Lumry, R.1    Rajender, S.2
  • 9
    • 0001176490 scopus 로고
    • Statistical Interpretation of Enthalpy-Entropy Compensation
    • Krug, R. R.; Hunter, W. G.; Grieger, R. A. Statistical Interpretation of Enthalpy-Entropy Compensation Nature 1976, 261, 566-567
    • (1976) Nature , vol.261 , pp. 566-567
    • Krug, R.R.1    Hunter, W.G.2    Grieger, R.A.3
  • 10
    • 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
    • (1995) Chem. Biol. , vol.2 , pp. 709-712
    • Dunitz, J.D.1
  • 11
    • 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
    • (2001) Protein Sci. , vol.10 , pp. 661-667
    • Sharp, K.1
  • 12
    • 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
    • (2013) Annu. Rev. Biophys. , vol.42 , pp. 121-142
    • Chodera, J.D.1    Mobley, D.L.2
  • 13
    • 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
    • (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
  • 14
    • 52049093186 scopus 로고    scopus 로고
    • Conformational Constraint in Protein Ligand Design and the Inconsistency of Binding Entropy
    • Udugamasooriya, D. G.; Spaller, M. R. Conformational Constraint in Protein Ligand Design and the Inconsistency of Binding Entropy Biopolymers 2008, 89, 653-667
    • (2008) Biopolymers , vol.89 , pp. 653-667
    • Udugamasooriya, D.G.1    Spaller, M.R.2
  • 16
    • 70450194691 scopus 로고    scopus 로고
    • Thermodynamic and Structural Effects of Conformational Constraints in Protein-Ligand Interactions. Entropic Paradoxy Associated with Ligand Preorganization
    • DeLorbe, J. E.; Clements, J. H.; Teresk, M. G.; Benfield, A. P.; Plake, H. R.; Millspaugh, L. E.; Martin, S. F. Thermodynamic and Structural Effects of Conformational Constraints in Protein-Ligand Interactions. Entropic Paradoxy Associated with Ligand Preorganization J. Am. Chem. Soc. 2009, 131, 16758-16770
    • (2009) J. Am. Chem. Soc. , vol.131 , pp. 16758-16770
    • Delorbe, J.E.1    Clements, J.H.2    Teresk, M.G.3    Benfield, A.P.4    Plake, H.R.5    Millspaugh, L.E.6    Martin, S.F.7
  • 18
    • 0000223084 scopus 로고
    • Thermodynamics of Molecular Recognition by Cyclodextrins. 1. Calorimetric Titration of Inclusion Complexation of Naphthalenesulfonates with α-, β-, and γ-Cyclodextrins: Enthalpy-Entropy Compensation
    • Inoue, Y.; Hakushi, T.; Liu, Y.; Tong, L.; Shen, B.; Jin, D. Thermodynamics of Molecular Recognition by Cyclodextrins. 1. Calorimetric Titration of Inclusion Complexation of Naphthalenesulfonates with α-, β-, and γ-Cyclodextrins: Enthalpy-Entropy Compensation J. Am. Chem. Soc. 1993, 115, 475-481
    • (1993) J. Am. Chem. Soc. , vol.115 , pp. 475-481
    • Inoue, Y.1    Hakushi, T.2    Liu, Y.3    Tong, L.4    Shen, B.5    Jin, D.6
  • 19
    • 0034630938 scopus 로고    scopus 로고
    • Chiral Recognition Thermodynamics of B-Cyclodextrin: The Thermodynamic Origin of Enantioselectivity and the Enthalpy-Entropy Compensation Effect
    • Rekharsky, M.; Inoue, Y. Chiral Recognition Thermodynamics of B-Cyclodextrin: The Thermodynamic Origin of Enantioselectivity and the Enthalpy-Entropy Compensation Effect J. Am. Chem. Soc. 2000, 122, 4418-4435
    • (2000) J. Am. Chem. Soc. , vol.122 , pp. 4418-4435
    • Rekharsky, M.1    Inoue, Y.2
  • 20
    • 0001386795 scopus 로고
    • Calorimetric Titration of Inclusion Complexation with Modified.beta.-Cyclodextrins. Enthalpy-Entropy Compensation in Host-Guest Complexation: From Ionophore to Cyclodextrin and Cyclophane
    • Inoue, Y.; Liu, Y.; Tong, L. H.; Shen, B. J.; Jin, D. S. Calorimetric Titration of Inclusion Complexation with Modified.beta.-Cyclodextrins. Enthalpy-Entropy Compensation in Host-Guest Complexation: From Ionophore to Cyclodextrin and Cyclophane J. Am. Chem. Soc. 1993, 115, 10637-10644
    • (1993) J. Am. Chem. Soc. , vol.115 , pp. 10637-10644
    • Inoue, Y.1    Liu, Y.2    Tong, L.H.3    Shen, B.J.4    Jin, D.S.5
  • 21
    • 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
    • (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
  • 22
    • 80054680901 scopus 로고    scopus 로고
    • Elucidating the Energetics of Entropically Driven Protein-Ligand Association: Calculations of Absolute Binding Free Energy and Entropy
    • Deng, N.; Zhang, P.; Cieplak, P.; Lai, L. Elucidating the Energetics of Entropically Driven Protein-Ligand Association: Calculations of Absolute Binding Free Energy and Entropy J. Phys. Chem. B 2011, 115, 11902-11910
    • (2011) J. Phys. Chem. B , vol.115 , pp. 11902-11910
    • Deng, N.1    Zhang, P.2    Cieplak, P.3    Lai, L.4
  • 23
    • 84856860496 scopus 로고    scopus 로고
    • Probing the Effect of Conformational Constraint on Phosphorylated Ligand Binding to an SH2 Domain Using Polarizable Force Field Simulations
    • Shi, Y.; Zhu, C. Z.; Martin, S. F.; Ren, P. Probing the Effect of Conformational Constraint on Phosphorylated Ligand Binding to an SH2 Domain Using Polarizable Force Field Simulations J. Phys. Chem. B 2012, 116, 1716-1727
    • (2012) J. Phys. Chem. B , vol.116 , pp. 1716-1727
    • Shi, Y.1    Zhu, C.Z.2    Martin, S.F.3    Ren, P.4
  • 25
    • 0032233055 scopus 로고    scopus 로고
    • Computer Simulations with Explicit Solvent: Recent Progress in the Thermodynamic Decomposition of Free Energies and in Modeling Electrostatic Effects
    • Levy, R. M.; Gallicchio, E. Computer Simulations with Explicit Solvent: Recent Progress in the Thermodynamic Decomposition of Free Energies and in Modeling Electrostatic Effects Annu. Rev. Phys. Chem. 1998, 49, 531-567
    • (1998) Annu. Rev. Phys. Chem. , vol.49 , pp. 531-567
    • Levy, R.M.1    Gallicchio, E.2
  • 26
    • 0038001529 scopus 로고    scopus 로고
    • Staging is More Important than Perturbation Method for Computation of Enthalpy and Entropy Changes in Complex Systems
    • Lu, N.; Kofke, D. A.; Woolf, T. B. Staging Is More Important than Perturbation Method for Computation of Enthalpy and Entropy Changes in Complex Systems J. Phys. Chem. B 2003, 107, 5598-5611
    • (2003) J. Phys. Chem. B , vol.107 , pp. 5598-5611
    • Lu, N.1    Kofke, D.A.2    Woolf, T.B.3
  • 28
    • 10844229225 scopus 로고    scopus 로고
    • Calculation of the Aqueous Solvation Energy and Entropy, as Well as Free Energy, of Simple Polar Solutes
    • Wan, S.; Stote, R. H.; Karplus, M. Calculation of the Aqueous Solvation Energy and Entropy, as Well as Free Energy, of Simple Polar Solutes J. Chem. Phys. 2004, 121, 9539-9548
    • (2004) J. Chem. Phys. , vol.121 , pp. 9539-9548
    • Wan, S.1    Stote, R.H.2    Karplus, M.3
  • 29
    • 77953782222 scopus 로고    scopus 로고
    • New Estimators for Calculating Solvation Entropy and Enthalpy and Comparative Assessments of Their Accuracy and Precision
    • Wyczalkowski, M. A.; Vitalis, A.; Pappu, R. V. New Estimators for Calculating Solvation Entropy and Enthalpy and Comparative Assessments of Their Accuracy and Precision J. Phys. Chem. B 2010, 114, 8166-8180
    • (2010) J. Phys. Chem. B , vol.114 , pp. 8166-8180
    • Wyczalkowski, M.A.1    Vitalis, A.2    Pappu, R.V.3
  • 30
    • 84904110938 scopus 로고    scopus 로고
    • Relative Binding Enthalpies from Molecular Dynamics Simulations Using a Direct Method
    • Roy, A.; Hua, D. P.; Ward, J. M.; Post, C. B. Relative Binding Enthalpies from Molecular Dynamics Simulations Using a Direct Method J. Chem. Theory Comput. 2014, 10 (7) 2759-2768 10.1021/ct500200n
    • (2014) J. Chem. Theory Comput. , vol.10 , Issue.7 , pp. 2759-2768
    • Roy, A.1    Hua, D.P.2    Ward, J.M.3    Post, C.B.4
  • 31
    • 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, 1-13
    • (2012) Theor. Chem. Acc. , vol.131 , pp. 1-13
    • Lai, B.1    Oostenbrink, C.2
  • 32
    • 84868214675 scopus 로고    scopus 로고
    • SPFP: Speed without Compromise-A Mixed Precision Model for GPU Accelerated Molecular Dynamics Simulations
    • Le Grand, S.; Götz, A. W.; Walker, R. C. SPFP: Speed without Compromise-A Mixed Precision Model for GPU Accelerated Molecular Dynamics Simulations Comput. Phys. Commun. 2013, 184, 374-380
    • (2013) Comput. Phys. Commun. , vol.184 , pp. 374-380
    • Le Grand, S.1    Götz, A.W.2    Walker, R.C.3
  • 33
    • 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
    • (2013) J. Chem. Theory Comput. , vol.9 , pp. 3878
    • Salomon-Ferrer, R.1    Götz, A.W.2    Poole, D.3    Le Grand, S.4    Walker, R.C.5
  • 38
    • 36649006642 scopus 로고    scopus 로고
    • Clustering Molecular Dynamics Trajectories: 1. Characterizing the Performance of Different Clustering Algorithms
    • Shao, J.; Tanner, S. W.; Thompson, N.; Cheatham, T. E. Clustering Molecular Dynamics Trajectories: 1. Characterizing the Performance of Different Clustering Algorithms J. Chem. Theory Comput. 2007, 3, 2312-2334
    • (2007) J. Chem. Theory Comput. , vol.3 , pp. 2312-2334
    • Shao, J.1    Tanner, S.W.2    Thompson, N.3    Cheatham, T.E.4
  • 40
    • 84890060319 scopus 로고    scopus 로고
    • How Much Do van der Waals Dispersion Forces Contribute to Molecular Recognition in Solution?
    • Yang, L.; Adam, C.; Nichol, G. S.; Cockroft, S. L. How Much Do van Der Waals Dispersion Forces Contribute to Molecular Recognition in Solution? Nat. Chem. 2013, 5, 1006-1010
    • (2013) Nat. Chem. , vol.5 , pp. 1006-1010
    • Yang, L.1    Adam, C.2    Nichol, G.S.3    Cockroft, S.L.4
  • 41
    • 12044259820 scopus 로고
    • Molecular Torsion Balance for Weak Molecular Recognition Forces. Effects of "tilted-T" Edge-to-Face Aromatic Interactions on Conformational Selection and Solid-State Structure
    • Paliwal, S.; Geib, S.; Wilcox, C. S. Molecular Torsion Balance for Weak Molecular Recognition Forces. Effects of "Tilted-T" Edge-to-Face Aromatic Interactions on Conformational Selection and Solid-State Structure J. Am. Chem. Soc. 1994, 116, 4497-4498
    • (1994) J. Am. Chem. Soc. , vol.116 , pp. 4497-4498
    • Paliwal, S.1    Geib, S.2    Wilcox, C.S.3
  • 42
    • 0035803745 scopus 로고    scopus 로고
    • Polarizabilities Inside Molecular Containers
    • Marquez, C.; Nau, W. M. Polarizabilities Inside Molecular Containers Angew. Chem., Int. Ed. 2001, 40, 4387-4390
    • (2001) Angew. Chem., Int. Ed. , vol.40 , pp. 4387-4390
    • Marquez, C.1    Nau, W.M.2
  • 43
    • 84897712486 scopus 로고    scopus 로고
    • Kinetics and Thermodynamics of Berberine Inclusion in Cucurbit[7]uril
    • Miskolczy, Z.; Biczók, L. Kinetics and Thermodynamics of Berberine Inclusion in Cucurbit[7]uril J. Phys. Chem. B 2014, 118, 2499
    • (2014) J. Phys. Chem. B , vol.118 , pp. 2499
    • Miskolczy, Z.1    Biczók, L.2
  • 44
    • 77953322826 scopus 로고    scopus 로고
    • Predicting Hydration Free Energies Using All-Atom Molecular Dynamics Simulations and Multiple Starting Conformations
    • Klimovich, P. V.; Mobley, D. L. Predicting Hydration Free Energies Using All-Atom Molecular Dynamics Simulations and Multiple Starting Conformations J. Comput.-Aided Mol. Des. 2010, 24, 307-316
    • (2010) J. Comput.-Aided Mol. Des. , vol.24 , pp. 307-316
    • Klimovich, P.V.1    Mobley, D.L.2
  • 45
    • 79951530217 scopus 로고    scopus 로고
    • Sources of the Deficiencies in the Popular SPC/E and TIP3P Models of Water
    • Kiss, P. T.; Baranyai, A. Sources of the Deficiencies in the Popular SPC/E and TIP3P Models of Water J. Chem. Phys. 2011, 134, 054106
    • (2011) J. Chem. Phys. , vol.134 , pp. 054106
    • Kiss, P.T.1    Baranyai, A.2
  • 46
    • 77950386243 scopus 로고    scopus 로고
    • Assessing the Thermodynamic Signatures of Hydrophobic Hydration for Several Common Water Models
    • Ashbaugh, H. S.; Collett, N. J.; Hatch, H. W.; Staton, J. A. Assessing the Thermodynamic Signatures of Hydrophobic Hydration for Several Common Water Models J. Chem. Phys. 2010, 132, 124504
    • (2010) J. Chem. Phys. , vol.132 , pp. 124504
    • Ashbaugh, H.S.1    Collett, N.J.2    Hatch, H.W.3    Staton, J.A.4
  • 47
    • 33748791718 scopus 로고    scopus 로고
    • Hydration Thermodynamic Properties of Amino Acid Analogues: A Systematic Comparison of Biomolecular Force Fields and Water Models
    • Hess, B.; van der Vegt, N. F. A. Hydration Thermodynamic Properties of Amino Acid Analogues: A Systematic Comparison of Biomolecular Force Fields and Water Models J. Phys. Chem. B 2006, 110, 17616-17626
    • (2006) J. Phys. Chem. B , vol.110 , pp. 17616-17626
    • Hess, B.1    Van Der Vegt, N.F.A.2
  • 48
    • 0032558365 scopus 로고    scopus 로고
    • Rationalization of the Dielectric Properties of Common Three-Site Water Models in Terms of Their Force Field Parameters
    • Höchtl, P.; Boresch, S.; Bitomsky, W.; Steinhauser, O. Rationalization of the Dielectric Properties of Common Three-Site Water Models in Terms of Their Force Field Parameters J. Chem. Phys. 1998, 109, 4927-4937
    • (1998) J. Chem. Phys. , vol.109 , pp. 4927-4937
    • Höchtl, P.1    Boresch, S.2    Bitomsky, W.3    Steinhauser, O.4
  • 49
    • 84867555063 scopus 로고    scopus 로고
    • Grid Inhomogeneous Solvation Theory: Hydration Structure and Thermodynamics of the Miniature Receptor cucurbit[7]uril
    • Nguyen, C. N.; Young, T. K.; Gilson, M. K. Grid Inhomogeneous Solvation Theory: Hydration Structure and Thermodynamics of the Miniature Receptor cucurbit[7]uril J. Chem. Phys. 2012, 137, 044101
    • (2012) J. Chem. Phys. , vol.137 , pp. 044101
    • Nguyen, C.N.1    Young, T.K.2    Gilson, M.K.3
  • 50
    • 39749178969 scopus 로고    scopus 로고
    • Predicting Small-Molecule Solvation Free Energies: An Informal Blind Test for Computational Chemistry
    • Nicholls, A.; Mobley, D. L.; Guthrie, J. P.; Chodera, J. D.; Bayly, C. I.; Cooper, M. D.; Pande, V. S. Predicting Small-Molecule Solvation Free Energies: An Informal Blind Test for Computational Chemistry J. Med. Chem. 2008, 51, 769-779
    • (2008) J. Med. Chem. , vol.51 , pp. 769-779
    • Nicholls, A.1    Mobley, D.L.2    Guthrie, J.P.3    Chodera, J.D.4    Bayly, C.I.5    Cooper, M.D.6    Pande, V.S.7
  • 51
    • 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
    • (2007) J. Phys. Chem. B , vol.111 , pp. 2242-2254
    • Mobley, D.L.1    Dumont, E.2    Chodera, J.D.3    Dill, K.A.4
  • 53
    • 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
    • (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
  • 54
    • 65249155929 scopus 로고    scopus 로고
    • A Blind Challenge for Computational Solvation Free Energies: Introduction and Overview
    • Guthrie, J. P. A Blind Challenge for Computational Solvation Free Energies: Introduction and Overview J. Phys. Chem. B 2009, 113, 4501-4507
    • (2009) J. Phys. Chem. B , vol.113 , pp. 4501-4507
    • Guthrie, J.P.1
  • 56
    • 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
    • (1996) J. Am. Chem. Soc. , vol.118 , pp. 11225-11236
    • Jorgensen, W.L.1    Maxwell, D.S.2    Tirado-Rives, J.3
  • 57
    • 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. 2013, 10, 273-281
    • (2013) J. Chem. Theory Comput. , vol.10 , pp. 273-281
    • Chapman, D.E.1    Steck, J.K.2    Nerenberg, P.S.3
  • 58
    • 74549181405 scopus 로고    scopus 로고
    • Kirkwood-Buff Derived Force Field for Alkali Chlorides in Simple Point Charge Water
    • Klasczyk, B.; Knecht, V. Kirkwood-Buff Derived Force Field for Alkali Chlorides in Simple Point Charge Water J. Chem. Phys. 2010, 132, 024109
    • (2010) J. Chem. Phys. , vol.132 , pp. 024109
    • Klasczyk, B.1    Knecht, V.2
  • 59
    • 33746679254 scopus 로고    scopus 로고
    • Chemical Potential Derivatives and Preferential Interaction Parameters in Biological Systems from Kirkwood-Buff Theory
    • Smith, P. E. Chemical Potential Derivatives and Preferential Interaction Parameters in Biological Systems from Kirkwood-Buff Theory Biophys. J. 2006, 91, 849-856
    • (2006) Biophys. J. , vol.91 , pp. 849-856
    • Smith, P.E.1
  • 60
    • 72049125389 scopus 로고    scopus 로고
    • Kirkwood-Buff Theory of Molecular and Protein Association, Aggregation, and Cellular Crowding
    • Gee, M. B.; Smith, P. E. Kirkwood-Buff Theory of Molecular and Protein Association, Aggregation, and Cellular Crowding J. Chem. Phys. 2009, 131, 165101
    • (2009) J. Chem. Phys. , vol.131 , pp. 165101
    • Gee, M.B.1    Smith, P.E.2
  • 61
    • 84884188204 scopus 로고    scopus 로고
    • Kirkwood-Buff Analysis of Aqueous N-Methylacetamide and Acetamide Solutions Modeled by the CHARMM Additive and Drude Polarizable Force Fields
    • Lin, B.; Lopes, P. E. M.; Roux, B.; A, D. M., Jr Kirkwood-Buff Analysis of Aqueous N-Methylacetamide and Acetamide Solutions Modeled by the CHARMM Additive and Drude Polarizable Force Fields J. Chem. Phys. 2013, 139, 084509
    • (2013) J. Chem. Phys. , vol.139 , pp. 084509
    • Lin, B.1    Lopes, P.E.M.2    Roux, B.3
  • 62
    • 84884200747 scopus 로고    scopus 로고
    • A Comparative Kirkwood-Buff Study of Aqueous Methanol Solutions Modeled by the CHARMM Additive and Drude Polarizable Force Fields
    • Lin, B.; He, X.; MacKerell, A. D. A Comparative Kirkwood-Buff Study of Aqueous Methanol Solutions Modeled by the CHARMM Additive and Drude Polarizable Force Fields J. Phys. Chem. B 2013, 117, 10572-10580
    • (2013) J. Phys. Chem. B , vol.117 , pp. 10572-10580
    • Lin, B.1    He, X.2    Mackerell, A.D.3
  • 63
    • 33646559968 scopus 로고    scopus 로고
    • The Paradoxical Thermodynamic Basis for the Interaction of Ethylene Glycol, Glycine, and Sarcosine Chains with Bovine Carbonic Anhydrase II: An Unexpected Manifestation of Enthalpy/Entropy Compensation
    • Krishnamurthy, V. M.; Bohall, B. R.; Semetey, V.; Whitesides, G. M. The Paradoxical Thermodynamic Basis for the Interaction of Ethylene Glycol, Glycine, and Sarcosine Chains with Bovine Carbonic Anhydrase II: An Unexpected Manifestation of Enthalpy/Entropy Compensation J. Am. Chem. Soc. 2006, 128, 5802-5812
    • (2006) J. Am. Chem. Soc. , vol.128 , pp. 5802-5812
    • Krishnamurthy, V.M.1    Bohall, B.R.2    Semetey, V.3    Whitesides, G.M.4
  • 65
    • 0031058541 scopus 로고    scopus 로고
    • The Statistical-Thermodynamic Basis for Computation of Binding Affinities: A Critical Review
    • Gilson, M. K.; Given, J. A.; Bush, B. L.; McCammon, J. A. The Statistical-Thermodynamic Basis for Computation of Binding Affinities: A Critical Review Biophys. J. 1997, 72, 1047-1069
    • (1997) Biophys. J. , vol.72 , pp. 1047-1069
    • Gilson, M.K.1    Given, J.A.2    Bush, B.L.3    McCammon, J.A.4
  • 66
    • 0029633155 scopus 로고
    • The Calculation of the Potential of Mean Force Using Computer Simulations
    • Roux, B. The Calculation of the Potential of Mean Force Using Computer Simulations Comput. Phys. Commun. 1995, 91, 275-282
    • (1995) Comput. Phys. Commun. , vol.91 , pp. 275-282
    • Roux, B.1
  • 67
    • 18744372751 scopus 로고    scopus 로고
    • Calculation of Absolute Protein-Ligand Binding Free Energy from Computer Simulations
    • Woo, H.-J.; Roux, B. Calculation of Absolute Protein-Ligand Binding Free Energy from Computer Simulations Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 6825-6830
    • (2005) Proc. Natl. Acad. Sci. U.S.A. , vol.102 , pp. 6825-6830
    • Woo, H.-J.1    Roux, B.2
  • 68
    • 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
    • (2013) J. Comput. Chem. , vol.34 , pp. 2360-2371
    • Velez-Vega, C.1    Gilson, M.K.2
  • 69
    • 38949107937 scopus 로고    scopus 로고
    • Molecular Dynamics Simulations of B-Cyclodextrin-Aziadamantane Complexes in Water
    • Sellner, B.; Zifferer, G.; Kornherr, A.; Krois, D.; Brinker, U. H. Molecular Dynamics Simulations of B-Cyclodextrin-Aziadamantane Complexes in Water J. Phys. Chem. B 2008, 112, 710-714
    • (2008) J. Phys. Chem. B , vol.112 , pp. 710-714
    • Sellner, B.1    Zifferer, G.2    Kornherr, A.3    Krois, D.4    Brinker, U.H.5
  • 70
    • 0031058541 scopus 로고    scopus 로고
    • The Statistical-Thermodynamic Basis for Computation of Binding Affinities: A Critical Review
    • Gilson, M. K.; Given, J. A.; Bush, B. L.; McCammon, J. A. The Statistical-Thermodynamic Basis for Computation of Binding Affinities: A Critical Review Biophys. J. 1997, 72, 1047-1069
    • (1997) Biophys. J. , vol.72 , pp. 1047-1069
    • Gilson, M.K.1    Given, J.A.2    Bush, B.L.3    McCammon, J.A.4
  • 71
    • 78650129666 scopus 로고    scopus 로고
    • Symmetry Numbers for Rigid, Flexible, and Fluxional Molecules: Theory and Applications
    • Gilson, M. K.; Irikura, K. K. Symmetry Numbers for Rigid, Flexible, and Fluxional Molecules: Theory and Applications J. Phys. Chem. B 2010, 114, 16304-16317
    • (2010) J. Phys. Chem. B , vol.114 , pp. 16304-16317
    • Gilson, M.K.1    Irikura, K.K.2
  • 72
    • 84862239263 scopus 로고    scopus 로고
    • Calculation of Host-Guest Binding Affinities Using a Quantum-Mechanical Energy Model
    • Muddana, H. S.; Gilson, M. K. Calculation of Host-Guest Binding Affinities Using a Quantum-Mechanical Energy Model J. Chem. Theory Comput. 2012, 8, 2023-2033
    • (2012) J. Chem. Theory Comput. , vol.8 , pp. 2023-2033
    • Muddana, H.S.1    Gilson, M.K.2
  • 74
    • 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
    • (2000) J. Comput. Chem. , vol.21 , pp. 132-146
    • Jakalian, A.1    Bush, B.L.2    Jack, D.B.3    Bayly, C.I.4
  • 75
    • 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
    • (2002) J. Comput. Chem. , vol.23 , pp. 1623-1641
    • Jakalian, A.1    Jack, D.B.2    Bayly, C.I.3
  • 76
    • 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. Graph. Modell. 2006, 25, 247-260
    • (2006) J. Mol. Graph. Modell. , vol.25 , pp. 247-260
    • Wang, J.1    Wang, W.2    Kollman, P.A.3    Case, D.A.4
  • 77
    • 70349956450 scopus 로고    scopus 로고
    • Molecular Dynamics Simulations of the Dynamic and Energetic Properties of Alkali and Halide Ions Using Water-Model-Specific Ion Parameters
    • Joung, I. S.; Cheatham, T. E. Molecular Dynamics Simulations of the Dynamic and Energetic Properties of Alkali and Halide Ions Using Water-Model-Specific Ion Parameters J. Phys. Chem. B 2009, 113, 13279-13290
    • (2009) J. Phys. Chem. B , vol.113 , pp. 13279-13290
    • Joung, I.S.1    Cheatham, T.E.2
  • 79
    • 84880022273 scopus 로고    scopus 로고
    • PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data
    • Roe, D. R.; Cheatham, T. E. PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data J. Chem. Theory Comput. 2013, 9, 3084-3095
    • (2013) J. Chem. Theory Comput. , vol.9 , pp. 3084-3095
    • Roe, D.R.1    Cheatham, T.E.2
  • 80
    • 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
    • (1989) J. Chem. Phys. , vol.91 , pp. 461-466
    • Flyvbjerg, H.1    Petersen, H.G.2
  • 81
    • 36649007647 scopus 로고    scopus 로고
    • Accurate and Efficient Corrections for Missing Dispersion Interactions in Molecular Simulations
    • Shirts, M. R.; Mobley, D. L.; Chodera, J. D.; Pande, V. S. Accurate and Efficient Corrections for Missing Dispersion Interactions in Molecular Simulations J. Phys. Chem. B 2007, 111, 13052-13063
    • (2007) J. Phys. Chem. B , vol.111 , pp. 13052-13063
    • Shirts, M.R.1    Mobley, D.L.2    Chodera, J.D.3    Pande, V.S.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.