메뉴 건너뛰기




Volumn 10, Issue 9, 2014, Pages 3617-3625

Estimating translational and orientational entropies using the K -nearest neighbors algorithm

Author keywords

[No Author keywords available]

Indexed keywords


EID: 84907199950     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/ct500415g     Document Type: Article
Times cited : (42)

References (49)
  • 1
    • 0001700714 scopus 로고    scopus 로고
    • Inhomogeneous fluid approach to solvation thermodynamics. 1. Theory
    • Lazaridis, T. Inhomogeneous fluid approach to solvation thermodynamics. 1. Theory J. Phys. Chem. B 1998, 102 (18) 3531-3541
    • (1998) J. Phys. Chem. B , vol.102 , Issue.18 , pp. 3531-3541
    • Lazaridis, T.1
  • 2
    • 0001700713 scopus 로고    scopus 로고
    • Inhomogeneous fluid approach to solvation thermodynamics. 2. Applications to simple fluids
    • Lazaridis, T. Inhomogeneous fluid approach to solvation thermodynamics. 2. Applications to simple fluids J. Phys. Chem. B 1998, 102 (18) 3542-3550
    • (1998) J. Phys. Chem. B , vol.102 , Issue.18 , pp. 3542-3550
    • Lazaridis, T.1
  • 3
    • 84862910105 scopus 로고    scopus 로고
    • Computing the thermodynamic contributions of interfacial water
    • Li, Z.; Lazaridis, T. Computing the thermodynamic contributions of interfacial water Methods Mol. Biol. 2012, 819, 393-404
    • (2012) Methods Mol. Biol. , vol.819 , pp. 393-404
    • Li, Z.1    Lazaridis, T.2
  • 4
    • 84860354431 scopus 로고    scopus 로고
    • Benchmarking the thermodynamic analysis of water molecules around a model beta sheet
    • Huggins, D. J. Benchmarking the thermodynamic analysis of water molecules around a model beta sheet J. Comput. Chem. 2012, 33 (15) 1383-1392
    • (2012) J. Comput. Chem. , vol.33 , Issue.15 , pp. 1383-1392
    • Huggins, D.J.1
  • 5
    • 33644527925 scopus 로고    scopus 로고
    • Thermodynamics of buried water clusters at a protein-ligand binding interface
    • Li, Z.; Lazaridis, T. Thermodynamics of buried water clusters at a protein-ligand binding interface J. Phys. Chem. B 2006, 110 (3) 1464-1475
    • (2006) J. Phys. Chem. B , vol.110 , Issue.3 , pp. 1464-1475
    • Li, Z.1    Lazaridis, T.2
  • 6
    • 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 (3) 808-813
    • (2007) Proc. Natl. Acad. Sci. U.S.A. , vol.104 , Issue.3 , pp. 808-813
    • Young, T.1    Abel, R.2    Kim, B.3    Berne, B.J.4    Friesner, R.A.5
  • 7
    • 80755150215 scopus 로고    scopus 로고
    • Thermodynamic Properties of Water Molecules at a Protein Protein Interaction Surface
    • Huggins, D. J.; Marsh, M.; Payne, M. C. Thermodynamic Properties of Water Molecules at a Protein Protein Interaction Surface J. Chem. Theory Comput. 2011, 7 (11) 3514-3522
    • (2011) J. Chem. Theory Comput. , vol.7 , Issue.11 , pp. 3514-3522
    • Huggins, D.J.1    Marsh, M.2    Payne, M.C.3
  • 8
    • 77950554182 scopus 로고    scopus 로고
    • Structural Properties of Hydration Shell Around Various Conformations of Simple Polypeptides
    • Czapiewski, D.; Zielkiewicz, J. Structural Properties of Hydration Shell Around Various Conformations of Simple Polypeptides J. Phys. Chem. B 2010, 114 (13) 4536-4550
    • (2010) J. Phys. Chem. B , vol.114 , Issue.13 , pp. 4536-4550
    • Czapiewski, D.1    Zielkiewicz, J.2
  • 9
    • 84988603747 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 (4) 044101
    • (2012) J. Chem. Phys. , vol.137 , Issue.4 , pp. 044101
    • Nguyen, C.N.1    Young, T.K.2    Gilson, M.K.3
  • 10
    • 84880154439 scopus 로고    scopus 로고
    • Assessing the Accuracy of Inhomogeneous Fluid Solvation Theory in Predicting Hydration Free Energies of Simple Solutes
    • Huggins, D. J.; Payne, M. C. Assessing the Accuracy of Inhomogeneous Fluid Solvation Theory in Predicting Hydration Free Energies of Simple Solutes J. Phys. Chem. B 2013, 117 (27) 8232-8244
    • (2013) J. Phys. Chem. B , vol.117 , Issue.27 , pp. 8232-8244
    • Huggins, D.J.1    Payne, M.C.2
  • 11
    • 0034713263 scopus 로고    scopus 로고
    • Solvent reorganization energy and entropy in hydrophobic hydration
    • Lazaridis, T. Solvent reorganization energy and entropy in hydrophobic hydration J. Phys. Chem. B 2000, 104 (20) 4964-4979
    • (2000) J. Phys. Chem. B , vol.104 , Issue.20 , pp. 4964-4979
    • Lazaridis, T.1
  • 12
    • 2142754018 scopus 로고    scopus 로고
    • Orientational correlations and entropy in liquid water
    • Lazaridis, T.; Karplus, M. Orientational correlations and entropy in liquid water J. Chem. Phys. 1996, 105 (10) 4294-4316
    • (1996) J. Chem. Phys. , vol.105 , Issue.10 , pp. 4294-4316
    • Lazaridis, T.1    Karplus, M.2
  • 13
    • 33645971315 scopus 로고    scopus 로고
    • Entropy-based measure of structural order in water
    • Esposito, R.; Saija, F.; Saitta, A. M.; Giaquinta, P. V. Entropy-based measure of structural order in water Phys. Rev. E 2006, 73 (4) 040502
    • (2006) Phys. Rev. e , vol.73 , Issue.4 , pp. 040502
    • Esposito, R.1    Saija, F.2    Saitta, A.M.3    Giaquinta, P.V.4
  • 14
    • 67650047673 scopus 로고    scopus 로고
    • Thermodynamic properties of liquid water: An application of a nonparametric approach to computing the entropy of a neat fluid
    • Wang, L.; Abel, R.; Friesner, R. A.; Berne, B. J. Thermodynamic properties of liquid water: an application of a nonparametric approach to computing the entropy of a neat fluid J. Chem. Theory Comput. 2009, 5 (6) 1462-1473
    • (2009) J. Chem. Theory Comput. , vol.5 , Issue.6 , pp. 1462-1473
    • Wang, L.1    Abel, R.2    Friesner, R.A.3    Berne, B.J.4
  • 16
    • 84859571593 scopus 로고    scopus 로고
    • Balanced and bias-corrected computation of conformational entropy differences for molecular trajectories
    • Numata, J.; Knapp, E.-W. Balanced and bias-corrected computation of conformational entropy differences for molecular trajectories J. Chem. Theory Comput. 2012, 8 (4) 1235-1245
    • (2012) J. Chem. Theory Comput. , vol.8 , Issue.4 , pp. 1235-1245
    • Numata, J.1    Knapp, E.-W.2
  • 18
    • 33847642496 scopus 로고    scopus 로고
    • Nearest-neighbor nonparametric method for estimating the configurational entropy of complex molecules
    • Hnizdo, V.; Darian, E.; Fedorowicz, A.; Demchuk, E.; Li, S.; Singh, H. Nearest-neighbor nonparametric method for estimating the configurational entropy of complex molecules J. Comput. Chem. 2007, 28 (3) 655-668
    • (2007) J. Comput. Chem. , vol.28 , Issue.3 , pp. 655-668
    • Hnizdo, V.1    Darian, E.2    Fedorowicz, A.3    Demchuk, E.4    Li, S.5    Singh, H.6
  • 19
    • 46449096350 scopus 로고    scopus 로고
    • Efficient calculation of configurational entropy from molecular simulations by combining the mutual-information expansion and nearest-neighbor methods
    • Hnizdo, V.; Tan, J.; Killian, B. J.; Gilson, M. K. Efficient calculation of configurational entropy from molecular simulations by combining the mutual-information expansion and nearest-neighbor methods J. Comput. Chem. 2008, 29 (10) 1605-1614
    • (2008) J. Comput. Chem. , vol.29 , Issue.10 , pp. 1605-1614
    • Hnizdo, V.1    Tan, J.2    Killian, B.J.3    Gilson, M.K.4
  • 20
    • 84892863219 scopus 로고    scopus 로고
    • Comparing distance metrics for rotation using the k-nearest neighbors algorithm for entropy estimation
    • Huggins, D. J. Comparing distance metrics for rotation using the k-nearest neighbors algorithm for entropy estimation J. Comput. Chem. 2014, 35 (5) 377-385
    • (2014) J. Comput. Chem. , vol.35 , Issue.5 , pp. 377-385
    • Huggins, D.J.1
  • 21
    • 36849122972 scopus 로고
    • High-Temperature Equation of State by a Perturbation Method. I. Nonpolar Gases
    • Zwanzig, R. W. High-Temperature Equation of State by a Perturbation Method. I. Nonpolar Gases J. Chem. Phys. 1954, 22, 1420
    • (1954) J. Chem. Phys. , vol.22 , pp. 1420
    • Zwanzig, R.W.1
  • 24
    • 29244471731 scopus 로고    scopus 로고
    • A general purpose model for the condensed phases of water: TIP4P/2005
    • Abascal, J. L. F.; Vega, C. A general purpose model for the condensed phases of water: TIP4P/2005 J. Chem. Phys. 2005, 123 (23) 234505
    • (2005) J. Chem. Phys. , vol.123 , Issue.23 , pp. 234505
    • Abascal, J.L.F.1    Vega, C.2
  • 26
    • 75649152815 scopus 로고    scopus 로고
    • Local Order, Energy, and Mobility of Water Molecules in the Hydration Shell of Small Peptides
    • Agarwal, M.; Kushwaha, H. R.; Chakravarty, C. Local Order, Energy, and Mobility of Water Molecules in the Hydration Shell of Small Peptides J. Phys. Chem. B 2010, 114 (1) 651-659
    • (2010) J. Phys. Chem. B , vol.114 , Issue.1 , pp. 651-659
    • Agarwal, M.1    Kushwaha, H.R.2    Chakravarty, C.3
  • 27
    • 36449003554 scopus 로고
    • Constant-Pressure Molecular-Dynamics Algorithms
    • Martyna, G. J.; Tobias, D. J.; Klein, M. L. Constant-Pressure Molecular-Dynamics Algorithms J. Chem. Phys. 1994, 101 (5) 4177-4189
    • (1994) J. Chem. Phys. , vol.101 , Issue.5 , pp. 4177-4189
    • Martyna, G.J.1    Tobias, D.J.2    Klein, M.L.3
  • 28
    • 36449007836 scopus 로고
    • Constant-Pressure Molecular-Dynamics Simulation - The Langevin Piston Method
    • Feller, S. E.; Zhang, Y. H.; Pastor, R. W.; Brooks, B. R. Constant-Pressure Molecular-Dynamics Simulation-the Langevin Piston Method J. Chem. Phys. 1995, 103 (11) 4613-4621
    • (1995) J. Chem. Phys. , vol.103 , Issue.11 , pp. 4613-4621
    • Feller, S.E.1    Zhang, Y.H.2    Pastor, R.W.3    Brooks, B.R.4
  • 31
    • 3943103200 scopus 로고
    • Standard thermodynamics of transfer. Uses and misuses
    • Ben-Naim, A. Standard thermodynamics of transfer. Uses and misuses J. Chem. Phys. 1978, 82 (7) 792-803
    • (1978) J. Chem. Phys. , vol.82 , Issue.7 , pp. 792-803
    • Ben-Naim, A.1
  • 32
    • 84907225440 scopus 로고
    • The periodic boundary condition in non-cubic MD cells: Wigner-Seitz cells with reflection symmetry
    • Smith, W. The periodic boundary condition in non-cubic MD cells: Wigner-Seitz cells with reflection symmetry CCP5 Inf. Q. Comput. Simul. Condens. Phases, Informal Newslett. 1983, 10, 37
    • (1983) CCP5 Inf. Q. Comput. Simul. Condens. Phases, Informal Newslett. , vol.10 , pp. 37
    • Smith, W.1
  • 35
    • 0000249851 scopus 로고
    • Avoiding Singularities and Numerical Instabilities in Free-Energy Calculations Based on Molecular Simulations
    • Beutler, T. C.; Mark, A. E.; Vanschaik, R. C.; Gerber, P. R.; van Gunsteren, W. F. Avoiding Singularities and Numerical Instabilities in Free-Energy Calculations Based on Molecular Simulations Chem. Phys. Lett. 1994, 222 (6) 529-539
    • (1994) Chem. Phys. Lett. , vol.222 , Issue.6 , pp. 529-539
    • Beutler, T.C.1    Mark, A.E.2    Vanschaik, R.C.3    Gerber, P.R.4    Van Gunsteren, W.F.5
  • 36
    • 36449002336 scopus 로고
    • Separation-Shifted Scaling, a New Scaling Method for Lennard-Jones Interactions in Thermodynamic Integration
    • Zacharias, M.; Straatsma, T. P.; Mccammon, J. A. Separation-Shifted Scaling, a New Scaling Method for Lennard-Jones Interactions in Thermodynamic Integration J. Chem. Phys. 1994, 100 (12) 9025-9031
    • (1994) J. Chem. Phys. , vol.100 , Issue.12 , pp. 9025-9031
    • Zacharias, M.1    Straatsma, T.P.2    McCammon, J.A.3
  • 37
    • 77955577540 scopus 로고    scopus 로고
    • Good practices in free-energy calculations
    • Pohorille, A.; Jarzynski, C.; Chipot, C. Good practices in free-energy calculations J. Phys. Chem. B 2010, 114 (32) 10235-10253
    • (2010) J. Phys. Chem. B , vol.114 , Issue.32 , pp. 10235-10253
    • Pohorille, A.1    Jarzynski, C.2    Chipot, C.3
  • 38
    • 5244304444 scopus 로고
    • Efficient Estimation of Free-Energy Differences from Monte-Carlo Data
    • Bennett, C. H. Efficient Estimation of Free-Energy Differences from Monte-Carlo Data J. Comput. Phys. 1976, 22 (2) 245-268
    • (1976) J. Comput. Phys. , vol.22 , Issue.2 , pp. 245-268
    • Bennett, C.H.1
  • 39
    • 84865069022 scopus 로고    scopus 로고
    • A Toolkit for the Analysis of Free-Energy Perturbation Calculations
    • Liu, P.; Dehez, F.; Cai, W. S.; Chipot, C. A Toolkit for the Analysis of Free-Energy Perturbation Calculations J. Chem. Theory Comput. 2012, 8 (8) 2606-2616
    • (2012) J. Chem. Theory Comput. , vol.8 , Issue.8 , pp. 2606-2616
    • Liu, P.1    Dehez, F.2    Cai, W.S.3    Chipot, C.4
  • 40
    • 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. Hydration thermodynamic properties of amino acid analogues: a systematic comparison of biomolecular force fields and water models J. Phys. Chem. B 2006, 110 (35) 17616-17626
    • (2006) J. Phys. Chem. B , vol.110 , Issue.35 , pp. 17616-17626
    • Hess, B.1    Van Der Vegt, N.F.2
  • 41
    • 0000078301 scopus 로고    scopus 로고
    • Effects of long-range electrostatic potential truncation on the free energy of ionic hydration
    • Ashbaugh, H. S.; Wood, R. H. Effects of long-range electrostatic potential truncation on the free energy of ionic hydration J. Chem. Phys. 1997, 106 (19) 8135-8139
    • (1997) J. Chem. Phys. , vol.106 , Issue.19 , pp. 8135-8139
    • Ashbaugh, H.S.1    Wood, R.H.2
  • 42
    • 79954589281 scopus 로고    scopus 로고
    • Computation of methodology-independent single-ion solvation properties from molecular simulations. III. Correction terms for the solvation free energies, enthalpies, entropies, heat capacities, volumes, compressibilities, and expansivities of solvated ions
    • Reif, M. M.; Hünenberger, P. H. Computation of methodology-independent single-ion solvation properties from molecular simulations. III. Correction terms for the solvation free energies, enthalpies, entropies, heat capacities, volumes, compressibilities, and expansivities of solvated ions J. Chem. Phys. 2011, 134 (14) 144103
    • (2011) J. Chem. Phys. , vol.134 , Issue.14 , pp. 144103
    • Reif, M.M.1    Hünenberger, P.H.2
  • 43
    • 84903362843 scopus 로고    scopus 로고
    • Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: An accurate correction scheme for electrostatic finite-size effects
    • Rocklin, G. J.; Mobley, D. L.; Dill, K. A.; Hünenberger, P. H. Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: An accurate correction scheme for electrostatic finite-size effects J. Chem. Phys. 2013, 139 (18) 184103
    • (2013) J. Chem. Phys. , vol.139 , Issue.18 , pp. 184103
    • Rocklin, G.J.1    Mobley, D.L.2    Dill, K.A.3    Hünenberger, P.H.4
  • 44
    • 84867344848 scopus 로고    scopus 로고
    • New interaction parameters for charged amino acid side chains in the GROMOS force field
    • Reif, M. M.; Hünenberger, P. H.; Oostenbrink, C. New interaction parameters for charged amino acid side chains in the GROMOS force field J. Chem. Theory Comput. 2012, 8 (10) 3705-3723
    • (2012) J. Chem. Theory Comput. , vol.8 , Issue.10 , pp. 3705-3723
    • Reif, M.M.1    Hünenberger, P.H.2    Oostenbrink, C.3
  • 46
    • 79953740433 scopus 로고    scopus 로고
    • Concise formulas for the area and volume of a hyperspherical cap
    • Li, S. Concise formulas for the area and volume of a hyperspherical cap Asian J. Math. Stat. 2011, 4 (1) 66-70
    • (2011) Asian J. Math. Stat. , vol.4 , Issue.1 , pp. 66-70
    • Li, S.1
  • 47
    • 33645903407 scopus 로고
    • Solvation thermodynamics of nonionic solutes
    • Ben-Naim, A.; Marcus, Y. Solvation thermodynamics of nonionic solutes J. Chem. Phys. 1984, 81 (4) 2016-2027
    • (1984) J. Chem. Phys. , vol.81 , Issue.4 , pp. 2016-2027
    • Ben-Naim, A.1    Marcus, Y.2
  • 48
    • 0017855698 scopus 로고
    • Interaction of the peptide bond with solvent water: A vapor phase analysis
    • Wolfenden, R. Interaction of the peptide bond with solvent water: a vapor phase analysis Biochemistry 1978, 17 (1) 201-204
    • (1978) Biochemistry , vol.17 , Issue.1 , pp. 201-204
    • Wolfenden, R.1
  • 49
    • 9944232242 scopus 로고
    • Group contributions to the thermodynamic properties of non-ionic organic solutes in dilute aqueous solution
    • Cabani, S.; Gianni, P.; Mollica, V.; Lepori, L. Group contributions to the thermodynamic properties of non-ionic organic solutes in dilute aqueous solution J. Solution Chem. 1981, 10 (8) 563-595
    • (1981) J. Solution Chem. , vol.10 , Issue.8 , pp. 563-595
    • Cabani, S.1    Gianni, P.2    Mollica, V.3    Lepori, L.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.