메뉴 건너뛰기




Volumn 9, Issue 8, 2013, Pages 3543-3556

Automated force field parameterization for nonpolarizable and polarizable atomic models based on ab initio target data

Author keywords

[No Author keywords available]

Indexed keywords


EID: 84882446110     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/ct4003477     Document Type: Article
Times cited : (202)

References (65)
  • 3
    • 0036725277 scopus 로고    scopus 로고
    • Molecular dynamics simulations of biomolecules
    • Karplus, M.; McCammon, J. A. Molecular dynamics simulations of biomolecules Nat. Struct. Biol. 2002, 9 (9) 646-652
    • (2002) Nat. Struct. Biol. , vol.9 , Issue.9 , pp. 646-652
    • Karplus, M.1    McCammon, J.A.2
  • 4
    • 0348244547 scopus 로고    scopus 로고
    • All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data
    • Foloppe, N.; MacKerell, A. D. All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data J. Comput. Chem. 2000, 21 (2) 86-104
    • (2000) J. Comput. Chem. , vol.21 , Issue.2 , pp. 86-104
    • Foloppe, N.1    MacKerell, A.D.2
  • 5
    • 0000214231 scopus 로고    scopus 로고
    • All-atom empirical force field for nucleic acids: II. Application to molecular dynamics simulations of DNA and RNA in solution
    • MacKerell, A. D.; Banavali, N. K. All-atom empirical force field for nucleic acids: II. Application to molecular dynamics simulations of DNA and RNA in solution J. Comput. Chem. 2000, 21 (2) 105-120
    • (2000) J. Comput. Chem. , vol.21 , Issue.2 , pp. 105-120
    • MacKerell, A.D.1    Banavali, N.K.2
  • 7
    • 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 simulations
    • 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 simulations J. Comput. Chem. 2004, 25 (11) 1400-1415
    • (2004) J. Comput. Chem. , vol.25 , Issue.11 , pp. 1400-1415
    • MacKerell, A.D.1    Feig, M.2    Brooks, C.L.3
  • 9
    • 0001398008 scopus 로고    scopus 로고
    • How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?
    • Wang, J. M.; Cieplak, P.; Kollman, P. A. How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? J. Comput. Chem. 2000, 21 (12) 1049-1074
    • (2000) J. Comput. Chem. , vol.21 , Issue.12 , pp. 1049-1074
    • Wang, J.M.1    Cieplak, P.2    Kollman, P.A.3
  • 10
    • 0035913529 scopus 로고    scopus 로고
    • Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides
    • Kaminski, G. A.; Friesner, R. A.; Tirado-Rives, J.; Jorgensen, W. L. Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides J. Phys. Chem. B 2001, 105 (28) 6474-6487
    • (2001) J. Phys. Chem. B , vol.105 , Issue.28 , pp. 6474-6487
    • Kaminski, G.A.1    Friesner, R.A.2    Tirado-Rives, J.3    Jorgensen, W.L.4
  • 11
    • 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 (13) 1656-1676
    • (2004) J. Comput. Chem. , vol.25 , Issue.13 , pp. 1656-1676
    • Oostenbrink, C.1    Villa, A.2    Mark, A.E.3    Van Gunsteren, W.F.4
  • 14
    • 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 (2) 132-146
    • (2000) J. Comput. Chem. , vol.21 , Issue.2 , pp. 132-146
    • Jakalian, A.1    Bush, B.L.2    Jack, D.B.3    Bayly, C.I.4
  • 15
    • 33748538349 scopus 로고    scopus 로고
    • Automatic atom type and bond type perception in molecular mechanical calculations
    • Wang, J. M.; 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 (2) 247-260
    • (2006) J. Mol. Graphics Modell. , vol.25 , Issue.2 , pp. 247-260
    • Wang, J.M.1    Wang, W.2    Kollman, P.A.3    Case, D.A.4
  • 16
    • 3142707941 scopus 로고    scopus 로고
    • Accuracy of free energies of hydration using CM1 and CM3 atomic charges
    • Udier-Blagovic, M.; De Tirado, P. M.; Pearlman, S. A.; Jorgensen, W. L. Accuracy of free energies of hydration using CM1 and CM3 atomic charges J. Comput. Chem. 2004, 25 (11) 1322-1332
    • (2004) J. Comput. Chem. , vol.25 , Issue.11 , pp. 1322-1332
    • Udier-Blagovic, M.1    De Tirado, P.M.2    Pearlman, S.A.3    Jorgensen, W.L.4
  • 18
    • 4444351490 scopus 로고    scopus 로고
    • Empirical force fields for biological macromolecules: Overview and issues
    • Mackerell, A. D. Empirical force fields for biological macromolecules: Overview and issues J. Comput. Chem. 2004, 25 (13) 1584-1604
    • (2004) J. Comput. Chem. , vol.25 , Issue.13 , pp. 1584-1604
    • MacKerell, A.D.1
  • 19
    • 3042524904 scopus 로고
    • A Well-Behaved Electrostatic Potential Based Method Using Charge Restraints for Deriving Atomic Charges - The Resp Model
    • Bayly, 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 (40) 10269-10280
    • (1993) J. Phys. Chem. , vol.97 , Issue.40 , pp. 10269-10280
    • Bayly, C.I.1    Cieplak, P.2    Cornell, W.D.3    Kollman, P.A.4
  • 20
    • 84862791277 scopus 로고    scopus 로고
    • Automation of AMOEBA polarizable force field parameterization for small molecules
    • Wu, J. C.; Chattree, G.; Ren, P. Y. Automation of AMOEBA polarizable force field parameterization for small molecules Theor. Chem. Acc. 2012, 131 (3) 1138
    • (2012) Theor. Chem. Acc. , vol.131 , Issue.3 , pp. 1138
    • Wu, J.C.1    Chattree, G.2    Ren, P.Y.3
  • 21
    • 84872142162 scopus 로고    scopus 로고
    • Systematic Parametrization of Polarizable Force Fields from Quantum Chemistry Data
    • Wang, L. P.; Chen, J. H.; Van Voorhis, T. Systematic Parametrization of Polarizable Force Fields from Quantum Chemistry Data J. Chem. Theory Comput. 2013, 9 (1) 452-460
    • (2013) J. Chem. Theory Comput. , vol.9 , Issue.1 , pp. 452-460
    • Wang, L.P.1    Chen, J.H.2    Van Voorhis, T.3
  • 22
    • 33645941402 scopus 로고
    • The Opls Potential Functions for Proteins - Energy Minimizations for Crystals of Cyclic-Peptides and Crambin
    • Jorgensen, W. L.; Tiradorives, J. The Opls Potential Functions for Proteins-Energy Minimizations for Crystals of Cyclic-Peptides and Crambin J. Am. Chem. Soc. 1988, 110 (6) 1657-1666
    • (1988) J. Am. Chem. Soc. , vol.110 , Issue.6 , pp. 1657-1666
    • Jorgensen, W.L.1    Tiradorives, J.2
  • 23
    • 0008075262 scopus 로고    scopus 로고
    • Atomistic Models and Force Fields
    • In, first ed. Becker, O. M. MacKerell, A. D. Roux, B. Watanabe, M. Eds; CRC Press: Boca Raton, FL
    • MacKerell, A. D. Atomistic Models and Force Fields. In Computational Biochemistry and Biophysics, first ed.; Becker, O. M.; MacKerell, A. D.; Roux, B.; Watanabe, M., Eds; CRC Press: Boca Raton, FL, 2001.
    • (2001) Computational Biochemistry and Biophysics
    • MacKerell, A.D.1
  • 24
    • 70449529413 scopus 로고    scopus 로고
    • Molecular modeling and dynamics studies with explicit inclusion of electronic polarizability: Theory and applications
    • Lopes, P. E. M.; Roux, B.; MacKerell, A. D. Molecular modeling and dynamics studies with explicit inclusion of electronic polarizability: theory and applications Theor. Chem. Acc. 2009, 124 (1-2) 11-28
    • (2009) Theor. Chem. Acc. , vol.124 , Issue.12 , pp. 11-28
    • Lopes, P.E.M.1    Roux, B.2    MacKerell, A.D.3
  • 25
    • 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 (1) 153-168
    • (2005) J. Chem. Theory Comput. , vol.1 , Issue.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
  • 26
    • 33846185169 scopus 로고    scopus 로고
    • Atomic level anisotropy in the electrostatic modeling of lone pairs for a polarizable force field based on the classical Drude oscillator
    • Harder, E.; Anisimov, V. M.; Vorobyov, I. V.; Lopes, P. E. M.; Noskov, S. Y.; MacKerell, A. D.; Roux, B. Atomic level anisotropy in the electrostatic modeling of lone pairs for a polarizable force field based on the classical Drude oscillator J. Chem. Theory Comput. 2006, 2 (6) 1587-1597
    • (2006) J. Chem. Theory Comput. , vol.2 , Issue.6 , pp. 1587-1597
    • Harder, E.1    Anisimov, V.M.2    Vorobyov, I.V.3    Lopes, P.E.M.4    Noskov, S.Y.5    MacKerell, A.D.6    Roux, B.7
  • 27
    • 30344482264 scopus 로고    scopus 로고
    • A polarizable model of water for molecular dynamics simulations of biomolecules
    • Lamoureux, G.; Harder, E.; Vorobyov, I. V.; Roux, B.; MacKerell, A. D. A polarizable model of water for molecular dynamics simulations of biomolecules Chem. Phys. Lett. 2006, 418 (1-3) 245-249
    • (2006) Chem. Phys. Lett. , vol.418 , Issue.13 , pp. 245-249
    • Lamoureux, G.1    Harder, E.2    Vorobyov, I.V.3    Roux, B.4    MacKerell, A.D.5
  • 28
    • 0041878923 scopus 로고    scopus 로고
    • Modeling induced polarization with classical Drude oscillators: Theory and molecular dynamics simulation algorithm
    • Lamoureux, G.; Roux, B. Modeling induced polarization with classical Drude oscillators: Theory and molecular dynamics simulation algorithm J. Chem. Phys. 2003, 119 (6) 3025-3039
    • (2003) J. Chem. Phys. , vol.119 , Issue.6 , pp. 3025-3039
    • Lamoureux, G.1    Roux, B.2
  • 29
    • 0141704114 scopus 로고    scopus 로고
    • A simple polarizable model of water based on classical Drude oscillators
    • Lamoureux, G.; MacKerell, A. D.; Roux, B. A simple polarizable model of water based on classical Drude oscillators J. Chem. Phys. 2003, 119 (10) 5185-5197
    • (2003) J. Chem. Phys. , vol.119 , Issue.10 , pp. 5185-5197
    • Lamoureux, G.1    MacKerell, A.D.2    Roux, B.3
  • 30
    • 33644879448 scopus 로고    scopus 로고
    • Absolute hydration free energy scale for alkali and halide ions established from simulations with a polarizable force field
    • Lamoureux, G.; Roux, B. Absolute hydration free energy scale for alkali and halide ions established from simulations with a polarizable force field J. Phys. Chem. B 2006, 110 (7) 3308-3322
    • (2006) J. Phys. Chem. B , vol.110 , Issue.7 , pp. 3308-3322
    • Lamoureux, G.1    Roux, B.2
  • 31
    • 36649037373 scopus 로고    scopus 로고
    • Polarizable empirical force field for the primary and secondary alcohol series based on the classical drude model
    • Anisimov, V. M.; Vorobyov, I. V.; Roux, B.; MacKerell, A. D. Polarizable empirical force field for the primary and secondary alcohol series based on the classical drude model J. Chem. Theory Comput. 2007, 3 (6) 1927-1946
    • (2007) J. Chem. Theory Comput. , vol.3 , Issue.6 , pp. 1927-1946
    • Anisimov, V.M.1    Vorobyov, I.V.2    Roux, B.3    MacKerell, A.D.4
  • 32
    • 34047226258 scopus 로고    scopus 로고
    • Polarizable empirical force field for aromatic compounds based on the classical drude oscillator
    • Lopes, P. E. M.; Lamoureux, G.; Roux, B.; MacKerell, A. D. Polarizable empirical force field for aromatic compounds based on the classical drude oscillator J. Phys. Chem. B 2007, 111 (11) 2873-2885
    • (2007) J. Phys. Chem. B , vol.111 , Issue.11 , pp. 2873-2885
    • Lopes, P.E.M.1    Lamoureux, G.2    Roux, B.3    MacKerell, A.D.4
  • 33
    • 77955368256 scopus 로고    scopus 로고
    • A Combined Experimental and Theoretical Study of Ion Solvation in Liquid N-Methylacetamide
    • Yu, H.; Mazzanti, C. L.; Whitfield, T. W.; Koeppe, R. E.; Andersen, O. S.; Roux, B. A Combined Experimental and Theoretical Study of Ion Solvation in Liquid N-Methylacetamide J. Am. Chem. Soc. 2010, 132 (31) 10847-10856
    • (2010) J. Am. Chem. Soc. , vol.132 , Issue.31 , pp. 10847-10856
    • Yu, H.1    Mazzanti, C.L.2    Whitfield, T.W.3    Koeppe, R.E.4    Andersen, O.S.5    Roux, B.6
  • 35
    • 0345720252 scopus 로고
    • Additivity Methods in Molecular Polarizability
    • Miller, K. J. Additivity Methods in Molecular Polarizability J. Am. Chem. Soc. 1990, 112 (23) 8533-8542
    • (1990) J. Am. Chem. Soc. , vol.112 , Issue.23 , pp. 8533-8542
    • Miller, K.J.1
  • 36
    • 84966262179 scopus 로고
    • Updating Quasi-Newton Matrices with Limited Storage
    • Nocedal, J. Updating Quasi-Newton Matrices with Limited Storage Math. Comput. 1980, 35 (151) 773-782
    • (1980) Math. Comput. , vol.35 , Issue.151 , pp. 773-782
    • Nocedal, J.1
  • 37
    • 33646887390 scopus 로고
    • On the Limited Memory Bfgs Method for Large-Scale Optimization
    • Liu, D. C.; Nocedal, J. On the Limited Memory Bfgs Method for Large-Scale Optimization Math. Program. 1989, 45 (3) 503-528
    • (1989) Math. Program. , vol.45 , Issue.3 , pp. 503-528
    • Liu, D.C.1    Nocedal, J.2
  • 39
    • 0026136104 scopus 로고
    • A Globally Convergent Augmented Lagrangian Algorithm for Optimization with General Constraints and Simple Bounds
    • Conn, A. R.; Gould, N. I. M.; Toint, P. L. A Globally Convergent Augmented Lagrangian Algorithm for Optimization with General Constraints and Simple Bounds SIAM J. Numer. Anal. 1991, 28 (2) 545-572
    • (1991) SIAM J. Numer. Anal. , vol.28 , Issue.2 , pp. 545-572
    • Conn, A.R.1    Gould, N.I.M.2    Toint, P.L.3
  • 40
    • 40249096072 scopus 로고    scopus 로고
    • Improving ultimate convergence of an augmented Lagrangian method
    • Birgin, E. G.; Martinez, J. M. Improving ultimate convergence of an augmented Lagrangian method Optim. Method. Softw. 2008, 23 (2) 177-195
    • (2008) Optim. Method. Softw. , vol.23 , Issue.2 , pp. 177-195
    • Birgin, E.G.1    Martinez, J.M.2
  • 41
    • 7544232432 scopus 로고    scopus 로고
    • Hydration of amino acid side chains: Nonpolar and electrostatic contributions calculated from staged molecular dynamics free energy simulations with explicit water molecules
    • Deng, Y. Q.; Roux, B. Hydration of amino acid side chains: Nonpolar and electrostatic contributions calculated from staged molecular dynamics free energy simulations with explicit water molecules J. Phys. Chem. B 2004, 108 (42) 16567-16576
    • (2004) J. Phys. Chem. B , vol.108 , Issue.42 , pp. 16567-16576
    • Deng, Y.Q.1    Roux, B.2
  • 42
    • 73949121918 scopus 로고    scopus 로고
    • Computation of Absolute Hydration and Binding Free Energy with Free Energy Perturbation Distributed Replica-Exchange Molecular Dynamics
    • Jiang, W.; Hodoscek, M.; Roux, B. Computation of Absolute Hydration and Binding Free Energy with Free Energy Perturbation Distributed Replica-Exchange Molecular Dynamics J. Chem. Theory Comput. 2009, 5 (10) 2583-2588
    • (2009) J. Chem. Theory Comput. , vol.5 , Issue.10 , pp. 2583-2588
    • Jiang, W.1    Hodoscek, M.2    Roux, B.3
  • 43
    • 65249147164 scopus 로고    scopus 로고
    • Computations of Absolute Solvation Free Energies of Small Molecules Using Explicit and Implicit Solvent Model
    • Shivakumar, D.; Deng, Y. Q.; Roux, B. Computations of Absolute Solvation Free Energies of Small Molecules Using Explicit and Implicit Solvent Model J. Chem. Theory Comput. 2009, 5 (4) 919-930
    • (2009) J. Chem. Theory Comput. , vol.5 , Issue.4 , pp. 919-930
    • Shivakumar, D.1    Deng, Y.Q.2    Roux, B.3
  • 44
    • 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 (1-2) 141-151
    • (1999) Chem. Phys. Lett. , vol.314 , Issue.12 , pp. 141-151
    • Sugita, Y.1    Okamoto, Y.2
  • 47
    • 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 (12) 10089-10092
    • (1993) J. Chem. Phys. , vol.98 , Issue.12 , pp. 10089-10092
    • Darden, T.1    York, D.2    Pedersen, L.3
  • 50
    • 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
  • 51
    • 84986440341 scopus 로고
    • Settle - An Analytical Version of the Shake and Rattle Algorithm for Rigid Water Models
    • Miyamoto, S.; Kollman, P. A. Settle-an Analytical Version of the Shake and Rattle Algorithm for Rigid Water Models J. Comput. Chem. 1992, 13 (8) 952-962
    • (1992) J. Comput. Chem. , vol.13 , Issue.8 , pp. 952-962
    • Miyamoto, S.1    Kollman, P.A.2
  • 52
    • 48749148224 scopus 로고
    • Rattle - A Velocity Version of the Shake Algorithm for Molecular-Dynamics Calculations
    • Andersen, H. C. Rattle-a Velocity Version of the Shake Algorithm for Molecular-Dynamics Calculations J. Comput. Phys. 1983, 52 (1) 24-34
    • (1983) J. Comput. Phys. , vol.52 , Issue.1 , pp. 24-34
    • Andersen, H.C.1
  • 53
    • 33646650705 scopus 로고
    • Reversible Multiple Time Scale Molecular-Dynamics
    • Tuckerman, M.; Berne, B. J.; Martyna, G. J. Reversible Multiple Time Scale Molecular-Dynamics J. Chem. Phys. 1992, 97 (3) 1990-2001
    • (1992) J. Chem. Phys. , vol.97 , Issue.3 , pp. 1990-2001
    • Tuckerman, M.1    Berne, B.J.2    Martyna, G.J.3
  • 54
    • 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 (1-3) 275-282
    • (1995) Comput. Phys. Commun. , vol.91 , Issue.13 , pp. 275-282
    • Roux, B.1
  • 55
    • 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 (45) 13052-13063
    • (2007) J. Phys. Chem. B , vol.111 , Issue.45 , pp. 13052-13063
    • Shirts, M.R.1    Mobley, D.L.2    Chodera, J.D.3    Pande, V.S.4
  • 56
    • 0000026966 scopus 로고    scopus 로고
    • Explicit reversible integrators for extended systems dynamics
    • Martyna, G. J.; Tuckerman, M. E.; Tobias, D. J.; Klein, M. L. Explicit reversible integrators for extended systems dynamics Mol. Phys. 1996, 87 (5) 1117-1157
    • (1996) Mol. Phys. , vol.87 , Issue.5 , pp. 1117-1157
    • Martyna, G.J.1    Tuckerman, M.E.2    Tobias, D.J.3    Klein, M.L.4
  • 58
    • 11144289562 scopus 로고    scopus 로고
    • Charge distribution in the water molecule - A comparison of methods
    • Martin, F.; Zipse, H. Charge distribution in the water molecule-A comparison of methods J. Comput. Chem. 2005, 26 (1) 97-105
    • (2005) J. Comput. Chem. , vol.26 , Issue.1 , pp. 97-105
    • Martin, F.1    Zipse, H.2
  • 60
    • 0141990949 scopus 로고    scopus 로고
    • Extremely precise free energy calculations of amino acid side chain analogs: Comparison of common molecular mechanics force fields for proteins
    • Shirts, M. R.; Pitera, J. W.; Swope, W. C.; Pande, V. S. Extremely precise free energy calculations of amino acid side chain analogs: Comparison of common molecular mechanics force fields for proteins J. Chem. Phys. 2003, 119 (11) 5740-5761
    • (2003) J. Chem. Phys. , vol.119 , Issue.11 , pp. 5740-5761
    • Shirts, M.R.1    Pitera, J.W.2    Swope, W.C.3    Pande, V.S.4
  • 61
    • 84860390173 scopus 로고    scopus 로고
    • Contributions of counter-charge in a potassium channel voltage-sensor domain
    • Pless, S. A.; Galpin, J. D.; Niciforovic, A. P.; Ahern, C. A. Contributions of counter-charge in a potassium channel voltage-sensor domain Nat. Chem. Biol. 2011, 7 (9) 617-623
    • (2011) Nat. Chem. Biol. , vol.7 , Issue.9 , pp. 617-623
    • Pless, S.A.1    Galpin, J.D.2    Niciforovic, A.P.3    Ahern, C.A.4
  • 63
    • 84872223512 scopus 로고    scopus 로고
    • Unnatural Amino Acids as Probes of Ligand-Receptor Interactions and Their Conformational Consequences
    • Pless, S. A.; Ahern, C. A. Unnatural Amino Acids as Probes of Ligand-Receptor Interactions and Their Conformational Consequences Annu. Rev. Pharmacol. Toxicol. 2013, 53, 211-229
    • (2013) Annu. Rev. Pharmacol. Toxicol. , vol.53 , pp. 211-229
    • Pless, S.A.1    Ahern, C.A.2
  • 64
    • 84857082110 scopus 로고    scopus 로고
    • CHARMM Additive All-Atom Force Field for Phosphate and Sulfate Linked to Carbohydrates
    • Mallajosyula, S. S.; Guvench, O.; Hatcher, E.; MacKerell, A. D. CHARMM Additive All-Atom Force Field for Phosphate and Sulfate Linked to Carbohydrates J. Chem. Theory Comput. 2012, 8 (2) 759-776
    • (2012) J. Chem. Theory Comput. , vol.8 , Issue.2 , pp. 759-776
    • Mallajosyula, S.S.1    Guvench, O.2    Hatcher, E.3    MacKerell, A.D.4
  • 65
    • 79955574923 scopus 로고    scopus 로고
    • version 1.3r1; Schrodinger, LLC. New York
    • The PyMOL Molecular Graphics System, version 1.3r1; Schrodinger, LLC.: New York, 2010.
    • (2010) The PyMOL Molecular Graphics System


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.