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Volumn 11, Issue 8, 2015, Pages 3714-3728

Refinement of Generalized Born Implicit Solvation Parameters for Nucleic Acids and Their Complexes with Proteins

Author keywords

[No Author keywords available]

Indexed keywords

DNA; NUCLEIC ACID; PROTEIN; PROTEIN BINDING; RNA; SOLVENT;

EID: 84938910994     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/acs.jctc.5b00271     Document Type: Article
Times cited : (53)

References (88)
  • 1
    • 84884931806 scopus 로고    scopus 로고
    • Twenty five years of nucleic acid simulations
    • Cheatham, T. E.; Case, D. A. Twenty five years of nucleic acid simulations Biopolymers 2013, 99 (12) 969-977 10.1002/bip.22331
    • (2013) Biopolymers , vol.99 , Issue.12 , pp. 969-977
    • Cheatham, T.E.1    Case, D.A.2
  • 2
    • 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 10.1063/1.464397
    • (1993) J. Chem. Phys. , vol.98 , Issue.12 , pp. 10089-10092
    • Darden, T.1    York, D.2    Pedersen, L.3
  • 4
    • 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.; 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 10.1002/1096-987X(200009)21:12<1049::AID-JCC3>3.0.CO;2-F
    • (2000) J. Comput. Chem. , vol.21 , Issue.12 , pp. 1049-1074
    • Wang, J.1    Cieplak, P.2    Kollman, P.A.3
  • 5
    • 0029170114 scopus 로고
    • Molecular Dynamics Simulations on Solvated Biomolecular Systems: The Particle Mesh Ewald Method Leads to Stable Trajectories of DNA, RNA, and Proteins
    • Cheatham, T. E., III; Miller, J. L.; Fox, T.; Darden, T. A.; Kollman, P. A. Molecular Dynamics Simulations on Solvated Biomolecular Systems: The Particle Mesh Ewald Method Leads to Stable Trajectories of DNA, RNA, and Proteins J. Am. Chem. Soc. 1995, 117 (14) 4193-4194 10.1021/ja00119a045
    • (1995) J. Am. Chem. Soc. , vol.117 , Issue.14 , pp. 4193-4194
    • Cheatham, T.E.1    Miller, J.L.2    Fox, T.3    Darden, T.A.4    Kollman, P.A.5
  • 6
    • 36749098380 scopus 로고    scopus 로고
    • Dynamics of B-DNA on the Microsecond Time Scale
    • Pérez, A.; Luque, F. J.; Orozco, M. Dynamics of B-DNA on the Microsecond Time Scale J. Am. Chem. Soc. 2007, 129 (47) 14739-14745 10.1021/ja0753546
    • (2007) J. Am. Chem. Soc. , vol.129 , Issue.47 , pp. 14739-14745
    • Pérez, A.1    Luque, F.J.2    Orozco, M.3
  • 7
    • 84923206685 scopus 로고    scopus 로고
    • Convergence and reproducibility in molecular dynamics simulations of the DNA duplex d(GCACGAACGAACGAACGC)
    • Galindo-Murillo, R.; Roe, D. R.; Cheatham, T. E. Convergence and reproducibility in molecular dynamics simulations of the DNA duplex d(GCACGAACGAACGAACGC) Biochim. Biophys. Acta, Gen. Subj. 2015, 1850 (5) 1041-1058 10.1016/j.bbagen.2014.09.007
    • (2015) Biochim. Biophys. Acta, Gen. Subj. , vol.1850 , Issue.5 , pp. 1041-1058
    • Galindo-Murillo, R.1    Roe, D.R.2    Cheatham, T.E.3
  • 8
    • 34250318638 scopus 로고    scopus 로고
    • Refinement of the AMBER Force Field for Nucleic Acids: Improving the Description of α/γ Conformers
    • Pérez, A.; Marchán, I.; Svozil, D.; Sponer, J.; Cheatham, T. E., III; Laughton, C. A.; Orozco, M. Refinement of the AMBER Force Field for Nucleic Acids: Improving the Description of α/γ Conformers Biophys. J. 2007, 92 (11) 3817-3829 10.1529/biophysj.106.097782
    • (2007) Biophys. J. , vol.92 , Issue.11 , pp. 3817-3829
    • Pérez, A.1    Marchán, I.2    Svozil, D.3    Sponer, J.4    Cheatham, T.E.5    Laughton, C.A.6    Orozco, M.7
  • 11
    • 33750035856 scopus 로고    scopus 로고
    • Improved efficiency of replica exchange simulations through use of a hybrid explicit/implicit solvation model
    • Okur, A.; Wickstrom, L.; Layten, M.; Geney, R.; Song, K.; Hornak, V.; Simmerling, C. Improved efficiency of replica exchange simulations through use of a hybrid explicit/implicit solvation model J. Chem. Theory Comput. 2006, 2 (2) 420-433 10.1021/ct050196z
    • (2006) J. Chem. Theory Comput. , vol.2 , Issue.2 , pp. 420-433
    • Okur, A.1    Wickstrom, L.2    Layten, M.3    Geney, R.4    Song, K.5    Hornak, V.6    Simmerling, C.7
  • 12
    • 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 10.1016/S0009-2614(99)01123-9
    • (1999) Chem. Phys. Lett. , vol.314 , Issue.1-2 , pp. 141-151
    • Sugita, Y.1    Okamoto, Y.2
  • 13
    • 0042561888 scopus 로고    scopus 로고
    • Solvent viscosity dependence of the folding rate of a small protein: Distributed computing study
    • Zagrovic, B.; Pande, V. Solvent viscosity dependence of the folding rate of a small protein: Distributed computing study J. Comput. Chem. 2003, 24 (12) 1432-1436 10.1002/jcc.10297
    • (2003) J. Comput. Chem. , vol.24 , Issue.12 , pp. 1432-1436
    • Zagrovic, B.1    Pande, V.2
  • 14
    • 0034701222 scopus 로고    scopus 로고
    • Molecular Dynamics Simulations of Nucleic Acids with a Generalized Born Solvation Model
    • Tsui, V.; Case, D. A. Molecular Dynamics Simulations of Nucleic Acids with a Generalized Born Solvation Model J. Am. Chem. Soc. 2000, 122 (11) 2489-2498 10.1021/ja9939385
    • (2000) J. Am. Chem. Soc. , vol.122 , Issue.11 , pp. 2489-2498
    • Tsui, V.1    Case, D.A.2
  • 16
    • 84860767348 scopus 로고    scopus 로고
    • Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born
    • Götz, A. W.; Williamson, M. J.; Xu, D.; Poole, D.; Le Grand, S.; Walker, R. C. Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born J. Chem. Theory Comput. 2012, 8 (5) 1542-1555 10.1021/ct200909j
    • (2012) J. Chem. Theory Comput. , vol.8 , Issue.5 , pp. 1542-1555
    • Götz, A.W.1    Williamson, M.J.2    Xu, D.3    Poole, D.4    Le Grand, S.5    Walker, R.C.6
  • 17
    • 33846783019 scopus 로고    scopus 로고
    • Structure and dynamics of the homologous series of alanine peptides: A joint molecular dynamics/NMR study
    • Graf, J.; Nguyen, P. H.; Stock, G.; Schwalbe, H. Structure and dynamics of the homologous series of alanine peptides: A joint molecular dynamics/NMR study J. Am. Chem. Soc. 2007, 129 (5) 1179-1189 10.1021/ja0660406
    • (2007) J. Am. Chem. Soc. , vol.129 , Issue.5 , pp. 1179-1189
    • Graf, J.1    Nguyen, P.H.2    Stock, G.3    Schwalbe, H.4
  • 18
    • 84907943526 scopus 로고    scopus 로고
    • Folding Simulations for Proteins with Diverse Topologies Are Accessible in Days with a Physics-Based Force Field and Implicit Solvent
    • Nguyen, H.; Maier, J.; Huang, H.; Perrone, V.; Simmerling, C. Folding Simulations for Proteins with Diverse Topologies Are Accessible in Days with a Physics-Based Force Field and Implicit Solvent J. Am. Chem. Soc. 2014, 136 (40) 13959-13962 10.1021/ja5032776
    • (2014) J. Am. Chem. Soc. , vol.136 , Issue.40 , pp. 13959-13962
    • Nguyen, H.1    Maier, J.2    Huang, H.3    Perrone, V.4    Simmerling, C.5
  • 19
    • 33749259954 scopus 로고    scopus 로고
    • Kinking occurs during molecular dynamics simulations of small DNA minicircles
    • Lankas, F.; Lavery, R.; Maddocks, J. H. Kinking occurs during molecular dynamics simulations of small DNA minicircles Structure 2006, 14 (10) 1527-1534 10.1016/j.str.2006.08.004
    • (2006) Structure , vol.14 , Issue.10 , pp. 1527-1534
    • Lankas, F.1    Lavery, R.2    Maddocks, J.H.3
  • 20
    • 79956013643 scopus 로고    scopus 로고
    • Atomistic simulations reveal bubbles, kinks and wrinkles in supercoiled DNA
    • Mitchell, J. S.; Laughton, C. A.; Harris, S. A. Atomistic simulations reveal bubbles, kinks and wrinkles in supercoiled DNA Nucleic Acids Res. 2011, 39 (9) 3928-3938 10.1093/nar/gkq1312
    • (2011) Nucleic Acids Res. , vol.39 , Issue.9 , pp. 3928-3938
    • Mitchell, J.S.1    Laughton, C.A.2    Harris, S.A.3
  • 21
    • 80054004071 scopus 로고    scopus 로고
    • Evaluation of DNA Force Fields in Implicit Solvation
    • Gaillard, T.; Case, D. A. Evaluation of DNA Force Fields in Implicit Solvation J. Chem. Theory Comput. 2011, 7 (10) 3181-3198 10.1021/ct200384r
    • (2011) J. Chem. Theory Comput. , vol.7 , Issue.10 , pp. 3181-3198
    • Gaillard, T.1    Case, D.A.2
  • 22
  • 23
    • 0037157693 scopus 로고    scopus 로고
    • Novel generalized Born methods
    • Lee, M. S.; Salsbury, F. R.; Brooks, C. L. Novel generalized Born methods J. Chem. Phys. 2002, 116 (24) 10606-10614 10.1063/1.1480013
    • (2002) J. Chem. Phys. , vol.116 , Issue.24 , pp. 10606-10614
    • Lee, M.S.1    Salsbury, F.R.2    Brooks, C.L.3
  • 24
    • 0038792211 scopus 로고    scopus 로고
    • New analytic approximation to the standard molecular volume definition and its application to generalized Born calculations
    • Lee, M. S.; Feig, M.; Salsbury, F. R.; Brooks, C. L. New analytic approximation to the standard molecular volume definition and its application to generalized Born calculations J. Comput. Chem. 2003, 24 (11) 1348-1356 10.1002/jcc.10272
    • (2003) J. Comput. Chem. , vol.24 , Issue.11 , pp. 1348-1356
    • Lee, M.S.1    Feig, M.2    Salsbury, F.R.3    Brooks, C.L.4
  • 25
    • 0141956090 scopus 로고    scopus 로고
    • Generalized born model with a simple smoothing function
    • Im, W.; Lee, M. S.; Brooks, C. L. Generalized born model with a simple smoothing function J. Comput. Chem. 2003, 24 (14) 1691-1702 10.1002/jcc.10321
    • (2003) J. Comput. Chem. , vol.24 , Issue.14 , pp. 1691-1702
    • Im, W.1    Lee, M.S.2    Brooks, C.L.3
  • 26
    • 0002636134 scopus 로고
    • Pairwise solute descreening of solute charges from a dielectric medium
    • Hawkins, G. D.; Cramer, C. J.; Truhlar, D. G. Pairwise solute descreening of solute charges from a dielectric medium Chem. Phys. Lett. 1995, 246 (1-2) 122-129 10.1016/0009-2614(95)01082-K
    • (1995) Chem. Phys. Lett. , vol.246 , Issue.1-2 , pp. 122-129
    • Hawkins, G.D.1    Cramer, C.J.2    Truhlar, D.G.3
  • 27
    • 1842479952 scopus 로고    scopus 로고
    • Exploring protein native states and large-scale conformational changes with a modified generalized born model
    • Onufriev, A.; Bashford, D.; Case, D. A. Exploring protein native states and large-scale conformational changes with a modified generalized born model Proteins: Struct., Funct., Genet. 2004, 55 (2) 383-394 10.1002/prot.20033
    • (2004) Proteins: Struct., Funct., Genet. , vol.55 , Issue.2 , pp. 383-394
    • Onufriev, A.1    Bashford, D.2    Case, D.A.3
  • 31
    • 80054004071 scopus 로고    scopus 로고
    • Evaluation of DNA Force Fields in Implicit Solvation
    • Gaillard, T.; Case, D. A. Evaluation of DNA Force Fields in Implicit Solvation J. Chem. Theory Comput. 2011, 7, 3181-3198 10.1021/ct200384r
    • (2011) J. Chem. Theory Comput. , vol.7 , pp. 3181-3198
    • Gaillard, T.1    Case, D.A.2
  • 32
    • 0032560959 scopus 로고    scopus 로고
    • Continuum Solvent Studies of the Stability of DNA, RNA, and Phosphoramidate-DNA Helices
    • Srinivasan, J.; Cheatham, T. E.; Cieplak, P.; Kollman, P. A.; Case, D. A. Continuum Solvent Studies of the Stability of DNA, RNA, and Phosphoramidate-DNA Helices J. Am. Chem. Soc. 1998, 120 (37) 9401-9409 10.1021/ja981844+
    • (1998) J. Am. Chem. Soc. , vol.120 , Issue.37 , pp. 9401-9409
    • Srinivasan, J.1    Cheatham, T.E.2    Cieplak, P.3    Kollman, P.A.4    Case, D.A.5
  • 33
    • 14244273182 scopus 로고    scopus 로고
    • Theory and applications of the generalized born solvation model in macromolecular simulations
    • Tsui, V.; Case, D. A. Theory and applications of the generalized born solvation model in macromolecular simulations Biopolymers 2000, 56 (4) 275-291 10.1002/1097-0282(2000)56:4<275::AID-BIP10024>3.0.CO;2-E
    • (2000) Biopolymers , vol.56 , Issue.4 , pp. 275-291
    • Tsui, V.1    Case, D.A.2
  • 34
    • 33845365528 scopus 로고    scopus 로고
    • A Computational Study of Nucleosomal DNA Flexibility
    • Ruscio, J. Z.; Onufriev, A. A Computational Study of Nucleosomal DNA Flexibility Biophys. J. 2006, 91 (11) 4121-4132 10.1529/biophysj.106.082099
    • (2006) Biophys. J. , vol.91 , Issue.11 , pp. 4121-4132
    • Ruscio, J.Z.1    Onufriev, A.2
  • 35
    • 1642419747 scopus 로고    scopus 로고
    • Improved Conformational Sampling through an Efficient Combination of Mean-Field Simulation Approaches
    • Cheng, X.; Hornak, V.; Simmerling, C. Improved Conformational Sampling through an Efficient Combination of Mean-Field Simulation Approaches J. Phys. Chem. B 2004, 108 (1) 426-437 10.1021/jp034505y
    • (2004) J. Phys. Chem. B , vol.108 , Issue.1 , pp. 426-437
    • Cheng, X.1    Hornak, V.2    Simmerling, C.3
  • 36
    • 0037120830 scopus 로고    scopus 로고
    • Conformational Heterogeneity Observed in Simulations of a Pyrene-Substituted DNA
    • Cui, G.; Simmerling, C. Conformational Heterogeneity Observed in Simulations of a Pyrene-Substituted DNA J. Am. Chem. Soc. 2002, 124 (41) 12154-12164 10.1021/ja026825l
    • (2002) J. Am. Chem. Soc. , vol.124 , Issue.41 , pp. 12154-12164
    • Cui, G.1    Simmerling, C.2
  • 37
    • 18544381108 scopus 로고    scopus 로고
    • Modified Replica Exchange Simulation Methods for Local Structure Refinement
    • Cheng, X.; Cui, G.; Hornak, V.; Simmerling, C. Modified Replica Exchange Simulation Methods for Local Structure Refinement J. Phys. Chem. B 2005, 109 (16) 8220-8230 10.1021/jp045437y
    • (2005) J. Phys. Chem. B , vol.109 , Issue.16 , pp. 8220-8230
    • Cheng, X.1    Cui, G.2    Hornak, V.3    Simmerling, C.4
  • 38
    • 0033064123 scopus 로고    scopus 로고
    • Unrestrained Stochastic Dynamics Simulations of the UUCG Tetraloop Using an Implicit Solvation Model
    • Williams, D. J.; Hall, K. B. Unrestrained Stochastic Dynamics Simulations of the UUCG Tetraloop Using an Implicit Solvation Model Biophys. J. 1999, 76 (6) 3192-3205 10.1016/S0006-3495(99)77471-0
    • (1999) Biophys. J. , vol.76 , Issue.6 , pp. 3192-3205
    • Williams, D.J.1    Hall, K.B.2
  • 39
    • 0345731284 scopus 로고    scopus 로고
    • Dynamics of the IRE RNA hairpin loop probed by 2-aminopurine fluorescence and stochastic dynamics simulations
    • Hall, K. B.; Williams, D. J. Dynamics of the IRE RNA hairpin loop probed by 2-aminopurine fluorescence and stochastic dynamics simulations RNA 2004, 10 (1) 34-47 10.1261/rna.5133404
    • (2004) RNA , vol.10 , Issue.1 , pp. 34-47
    • Hall, K.B.1    Williams, D.J.2
  • 40
    • 84988087911 scopus 로고
    • Calculating the electrostatic potential of molecules in solution: Method and error assessment
    • Gilson, M. K.; Sharp, K. A.; Honig, B. H. Calculating the electrostatic potential of molecules in solution: Method and error assessment J. Comput. Chem. 1988, 9 (4) 327-335 10.1002/jcc.540090407
    • (1988) J. Comput. Chem. , vol.9 , Issue.4 , pp. 327-335
    • Gilson, M.K.1    Sharp, K.A.2    Honig, B.H.3
  • 41
    • 0346971105 scopus 로고    scopus 로고
    • Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures
    • Feig, M.; Onufriev, A.; Lee, M. S.; Im, W.; Case, D. A.; Charles, L.; Brooks, I. Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures J. Comput. Chem. 2004, 25 (2) 265-284 10.1002/jcc.10378
    • (2004) J. Comput. Chem. , vol.25 , Issue.2 , pp. 265-284
    • Feig, M.1    Onufriev, A.2    Lee, M.S.3    Im, W.4    Case, D.A.5    Charles, L.6    Brooks, I.7
  • 42
    • 33645703426 scopus 로고    scopus 로고
    • Balancing an accurate representation of the molecular surface in generalized born formalisms with integrator stability in molecular dynamics simulations
    • Chocholoušová, J.; Feig, M. Balancing an accurate representation of the molecular surface in generalized born formalisms with integrator stability in molecular dynamics simulations J. Comput. Chem. 2006, 27 (6) 719-729 10.1002/jcc.20387
    • (2006) J. Comput. Chem. , vol.27 , Issue.6 , pp. 719-729
    • Chocholoušová, J.1    Feig, M.2
  • 43
    • 0001585978 scopus 로고    scopus 로고
    • Improving efficiency of large time-scale molecular dynamics simulations of hydrogen-rich systems
    • Feenstra, K. A.; Hess, B.; Berendsen, H. J. C. Improving efficiency of large time-scale molecular dynamics simulations of hydrogen-rich systems J. Comput. Chem. 1999, 20 (8) 786-798 10.1002/(SICI)1096-987X(199906)20:8<786::AID-JCC5>3.3.CO;2-2
    • (1999) J. Comput. Chem. , vol.20 , Issue.8 , pp. 786-798
    • Feenstra, K.A.1    Hess, B.2    Berendsen, H.J.C.3
  • 44
    • 33847723384 scopus 로고    scopus 로고
    • Secondary Structure Bias in Generalized Born Solvent Models: Comparison of Conformational Ensembles and Free Energy of Solvent Polarization from Explicit and Implicit Solvation
    • Roe, D. R.; Okur, A.; Wickstrom, L.; Hornak, V.; Simmerling, C. Secondary Structure Bias in Generalized Born Solvent Models: Comparison of Conformational Ensembles and Free Energy of Solvent Polarization from Explicit and Implicit Solvation J. Phys. Chem. B 2007, 111 (7) 1846-1857 10.1021/jp066831u
    • (2007) J. Phys. Chem. B , vol.111 , Issue.7 , pp. 1846-1857
    • Roe, D.R.1    Okur, A.2    Wickstrom, L.3    Hornak, V.4    Simmerling, C.5
  • 45
    • 33847713183 scopus 로고    scopus 로고
    • Generalized Born Model with a Simple, Robust Molecular Volume Correction
    • Mongan, J.; Simmerling, C.; McCammon, J. A.; Case, D. A.; Onufriev, A. Generalized Born Model with a Simple, Robust Molecular Volume Correction J. Chem. Theory Comput. 2007, 3 (1) 156-169 10.1021/ct600085e
    • (2007) J. Chem. Theory Comput. , vol.3 , Issue.1 , pp. 156-169
    • Mongan, J.1    Simmerling, C.2    McCammon, J.A.3    Case, D.A.4    Onufriev, A.5
  • 46
    • 46749105987 scopus 로고    scopus 로고
    • A Test on Peptide Stability of AMBER Force Fields with Implicit Solvation
    • Shell, M. S.; Ritterson, R.; Dill, K. A. A Test on Peptide Stability of AMBER Force Fields with Implicit Solvation J. Phys. Chem. B 2008, 112 (22) 6878-6886 10.1021/jp800282x
    • (2008) J. Phys. Chem. B , vol.112 , Issue.22 , pp. 6878-6886
    • Shell, M.S.1    Ritterson, R.2    Dill, K.A.3
  • 47
    • 84875983100 scopus 로고    scopus 로고
    • Improved Generalized Born Solvent Model Parameters for Protein Simulations
    • Nguyen, H.; Roe, D. R.; Simmerling, C. Improved Generalized Born Solvent Model Parameters for Protein Simulations J. Chem. Theory Comput. 2013, 9 (4) 2020-2034 10.1021/ct3010485
    • (2013) J. Chem. Theory Comput. , vol.9 , Issue.4 , pp. 2020-2034
    • Nguyen, H.1    Roe, D.R.2    Simmerling, C.3
  • 48
    • 84873526912 scopus 로고    scopus 로고
    • To milliseconds and beyond: challenges in the simulation of protein folding
    • Lane, T. J.; Shukla, D.; Beauchamp, K. A.; Pande, V. S. To milliseconds and beyond: challenges in the simulation of protein folding Curr. Opin. Struct. Biol. 2013, 23 (1) 58-65 10.1016/j.sbi.2012.11.002
    • (2013) Curr. Opin. Struct. Biol. , vol.23 , Issue.1 , pp. 58-65
    • Lane, T.J.1    Shukla, D.2    Beauchamp, K.A.3    Pande, V.S.4
  • 49
    • 42049087036 scopus 로고    scopus 로고
    • Implicit modeling of nonpolar solvation for simulating protein folding and conformational transitions
    • Chen, J.; Brooks, C. L. Implicit modeling of nonpolar solvation for simulating protein folding and conformational transitions Phys. Chem. Chem. Phys. 2008, 10 (4) 471-481 10.1039/B714141F
    • (2008) Phys. Chem. Chem. Phys. , vol.10 , Issue.4 , pp. 471-481
    • Chen, J.1    Brooks, C.L.2
  • 50
    • 73349107159 scopus 로고    scopus 로고
    • The AGBNP2 Implicit Solvation Model
    • Gallicchio, E.; Paris, K.; Levy, R. M. The AGBNP2 Implicit Solvation Model J. Chem. Theory Comput. 2009, 5 (9) 2544-2564 10.1021/ct900234u
    • (2009) J. Chem. Theory Comput. , vol.5 , Issue.9 , pp. 2544-2564
    • Gallicchio, E.1    Paris, K.2    Levy, R.M.3
  • 51
    • 0042208326 scopus 로고    scopus 로고
    • On the Nonpolar Hydration Free Energy of Proteins: Surface Area and Continuum Solvent Models for the Solute-Solvent Interaction Energy
    • Levy, R. M.; Zhang, L. Y.; Gallicchio, E.; Felts, A. K. On the Nonpolar Hydration Free Energy of Proteins: Surface Area and Continuum Solvent Models for the Solute-Solvent Interaction Energy J. Am. Chem. Soc. 2003, 125 (31) 9523-9530 10.1021/ja029833a
    • (2003) J. Am. Chem. Soc. , vol.125 , Issue.31 , pp. 9523-9530
    • Levy, R.M.1    Zhang, L.Y.2    Gallicchio, E.3    Felts, A.K.4
  • 52
    • 33744822783 scopus 로고    scopus 로고
    • Assessing implicit models for nonpolar mean solvation forces: The importance of dispersion and volume terms
    • Wagoner, J. A.; Baker, N. A. Assessing implicit models for nonpolar mean solvation forces: The importance of dispersion and volume terms Proc. Natl. Acad. Sci. U. S. A. 2006, 103 (22) 8331-8336 10.1073/pnas.0600118103
    • (2006) Proc. Natl. Acad. Sci. U. S. A. , vol.103 , Issue.22 , pp. 8331-8336
    • Wagoner, J.A.1    Baker, N.A.2
  • 53
    • 4444323489 scopus 로고    scopus 로고
    • Solvation forces on biomolecular structures: A comparison of explicit solvent and Poisson-Boltzmann models
    • Wagoner, J.; Baker, N. A. Solvation forces on biomolecular structures: A comparison of explicit solvent and Poisson-Boltzmann models J. Comput. Chem. 2004, 25 (13) 1623-1629 10.1002/jcc.20089
    • (2004) J. Comput. Chem. , vol.25 , Issue.13 , pp. 1623-1629
    • Wagoner, J.1    Baker, N.A.2
  • 54
    • 0344778061 scopus 로고
    • Semianalytical treatment of solvation for molecular mechanics and dynamics
    • Still, W. C.; Tempczyk, A.; Hawley, R. C.; Hendrickson, T. Semianalytical treatment of solvation for molecular mechanics and dynamics J. Am. Chem. Soc. 1990, 112 (16) 6127-6129 10.1021/ja00172a038
    • (1990) J. Am. Chem. Soc. , vol.112 , Issue.16 , pp. 6127-6129
    • Still, W.C.1    Tempczyk, A.2    Hawley, R.C.3    Hendrickson, T.4
  • 55
    • 36148936033 scopus 로고    scopus 로고
    • Analysis of integral expressions for effective Born radii
    • Mongan, J.; Svrcek-Seiler, W. A.; Onufriev, A. Analysis of integral expressions for effective Born radii J. Chem. Phys. 2007, 127 (18) 185101 10.1063/1.2783847
    • (2007) J. Chem. Phys. , vol.127 , Issue.18 , pp. 185101
    • Mongan, J.1    Svrcek-Seiler, W.A.2    Onufriev, A.3
  • 56
    • 0141453063 scopus 로고    scopus 로고
    • Deficiency of the Coulomb-field approximation in the generalized Born model: An improved formula for Born radii evaluation
    • Grycuk, T. Deficiency of the Coulomb-field approximation in the generalized Born model: An improved formula for Born radii evaluation J. Chem. Phys. 2003, 119 (9) 4817-4826 10.1063/1.1595641
    • (2003) J. Chem. Phys. , vol.119 , Issue.9 , pp. 4817-4826
    • Grycuk, T.1
  • 57
    • 78651330129 scopus 로고    scopus 로고
    • Reducing the Secondary Structure Bias in the Generalized Born Model via R6 Effective Radii
    • Aguilar, B.; Shadrach, R.; Onufriev, A. V. Reducing the Secondary Structure Bias in the Generalized Born Model via R6 Effective Radii J. Chem. Theory Comput. 2010, 6 (12) 3613-3630 10.1021/ct100392h
    • (2010) J. Chem. Theory Comput. , vol.6 , Issue.12 , pp. 3613-3630
    • Aguilar, B.1    Shadrach, R.2    Onufriev, A.V.3
  • 58
    • 0037110472 scopus 로고    scopus 로고
    • Effective Born radii in the generalized Born approximation: The importance of being perfect
    • Onufriev, A.; Case, D. A.; Bashford, D. Effective Born radii in the generalized Born approximation: The importance of being perfect J. Comput. Chem. 2002, 23 (14) 1297-1304 10.1002/jcc.10126
    • (2002) J. Comput. Chem. , vol.23 , Issue.14 , pp. 1297-1304
    • Onufriev, A.1    Case, D.A.2    Bashford, D.3
  • 59
    • 14544285906 scopus 로고    scopus 로고
    • Comparative Study of Generalized Born Models:Born Radii and Peptide Folding
    • Zhu, J.; Alexov, E.; Honig, B. Comparative Study of Generalized Born Models:Born Radii and Peptide Folding J. Phys. Chem. B 2005, 109 (7) 3008-3022 10.1021/jp046307s
    • (2005) J. Phys. Chem. B , vol.109 , Issue.7 , pp. 3008-3022
    • Zhu, J.1    Alexov, E.2    Honig, B.3
  • 60
    • 33846538819 scopus 로고    scopus 로고
    • The NEWUOA software for unconstrained optimization without derivatives
    • Pillo, G. Roma, M. Springer
    • Powell, M. J. D. The NEWUOA software for unconstrained optimization without derivatives. In Large-Scale Nonlinear Optimization; Pillo, G.; Roma, M., Eds.; Springer: 2006; Vol. 83, pp 255-297.
    • (2006) Large-Scale Nonlinear Optimization , vol.83 , pp. 255-297
    • Powell, M.J.D.1
  • 61
    • 84879693300 scopus 로고    scopus 로고
    • Derivative-free optimization: a review of algorithms and comparison of software implementations
    • Rios, L.; Sahinidis, N. Derivative-free optimization: a review of algorithms and comparison of software implementations J Glob Optim 2013, 56 (3) 1247-1293 10.1007/s10898-012-9951-y
    • (2013) J Glob Optim , vol.56 , Issue.3 , pp. 1247-1293
    • Rios, L.1    Sahinidis, N.2
  • 62
    • 0041711007 scopus 로고    scopus 로고
    • UOBYQA: unconstrained optimization by quadratic approximation
    • Powell, M. J. D. UOBYQA: unconstrained optimization by quadratic approximation Math. Program. 2002, 92 (3) 555-582 10.1007/s101070100290
    • (2002) Math. Program. , vol.92 , Issue.3 , pp. 555-582
    • Powell, M.J.D.1
  • 63
    • 0030953141 scopus 로고    scopus 로고
    • Molecular Dynamics Simulations Highlight the Structural Differences among DNA:DNA, RNA:RNA, and DNA:RNA Hybrid Duplexes
    • Cheatham, T. E.; Kollman, P. A. Molecular Dynamics Simulations Highlight the Structural Differences among DNA:DNA, RNA:RNA, and DNA:RNA Hybrid Duplexes J. Am. Chem. Soc. 1997, 119 (21) 4805-4825 10.1021/ja963641w
    • (1997) J. Am. Chem. Soc. , vol.119 , Issue.21 , pp. 4805-4825
    • Cheatham, T.E.1    Kollman, P.A.2
  • 64
    • 0004016501 scopus 로고
    • Comparison of simple potential functions for simulating liquid water
    • Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. Comparison of simple potential functions for simulating liquid water J. Chem. Phys. 1983, 79 (2) 926-935 10.1063/1.445869
    • (1983) J. Chem. Phys. , vol.79 , Issue.2 , pp. 926-935
    • Jorgensen, W.L.1    Chandrasekhar, J.2    Madura, J.D.3    Impey, R.W.4    Klein, M.L.5
  • 66
    • 0032530719 scopus 로고    scopus 로고
    • A novel mode of DNA recognition by a β-sheet revealed by the solution structure of the GCC-box binding domain in complex with DNA
    • Allen, M. D.; Yamasaki, K.; Ohme Takagi, M.; Tateno, M.; Suzuki, M. A novel mode of DNA recognition by a β-sheet revealed by the solution structure of the GCC-box binding domain in complex with DNA EMBO J. 1998, 17 (18) 5484-5496 10.1093/emboj/17.18.5484
    • (1998) EMBO J. , vol.17 , Issue.18 , pp. 5484-5496
    • Allen, M.D.1    Yamasaki, K.2    Ohme Takagi, M.3    Tateno, M.4    Suzuki, M.5
  • 67
    • 42449095007 scopus 로고    scopus 로고
    • Towards a molecular dynamics consensus view of B-DNA flexibility
    • Pérez, A.; Lankas, F.; Luque, F. J.; Orozco, M. Towards a molecular dynamics consensus view of B-DNA flexibility Nucleic Acids Res. 2008, 36 (7) 2379-2394 10.1093/nar/gkn082
    • (2008) Nucleic Acids Res. , vol.36 , Issue.7 , pp. 2379-2394
    • Pérez, A.1    Lankas, F.2    Luque, F.J.3    Orozco, M.4
  • 68
    • 0028800948 scopus 로고
    • Structure of a single-cytidine hairpin loop formed by the DNA triplet GCA
    • Zhu, L.; Chou, S.-H.; Xu, J.; Reid, B. R. Structure of a single-cytidine hairpin loop formed by the DNA triplet GCA Nat. Struct. Biol. 1995, 2 (11) 1012-1017 10.1038/nsb1195-1012
    • (1995) Nat. Struct. Biol. , vol.2 , Issue.11 , pp. 1012-1017
    • Zhu, L.1    Chou, S.-H.2    Xu, J.3    Reid, B.R.4
  • 69
    • 80455168345 scopus 로고    scopus 로고
    • Role of the closing base pair for d(GCA) hairpin stability: free energy analysis and folding simulations
    • Kannan, S.; Zacharias, M. Role of the closing base pair for d(GCA) hairpin stability: free energy analysis and folding simulations Nucleic Acids Res. 2011, 39 (19) 8271-8280 10.1093/nar/gkr541
    • (2011) Nucleic Acids Res. , vol.39 , Issue.19 , pp. 8271-8280
    • Kannan, S.1    Zacharias, M.2
  • 70
    • 77449092763 scopus 로고    scopus 로고
    • High-resolution NMR structure of an RNA model system: the 14-mer cUUCGg tetraloop hairpin RNA
    • Nozinovic, S.; Fürtig, B.; Jonker, H. R. A.; Richter, C.; Schwalbe, H. High-resolution NMR structure of an RNA model system: the 14-mer cUUCGg tetraloop hairpin RNA Nucleic Acids Res. 2010, 38 (2) 683-694 10.1093/nar/gkp956
    • (2010) Nucleic Acids Res. , vol.38 , Issue.2 , pp. 683-694
    • Nozinovic, S.1    Fürtig, B.2    Jonker, H.R.A.3    Richter, C.4    Schwalbe, H.5
  • 71
    • 22144496413 scopus 로고    scopus 로고
    • Does water play a structural role in the folding of small nucleic acids?
    • Sorin, E. J.; Rhee, Y. M.; Pande, V. S. Does water play a structural role in the folding of small nucleic acids? Biophys. J. 2005, 88 (4) 2516-2524 10.1529/biophysj.104.055087
    • (2005) Biophys. J. , vol.88 , Issue.4 , pp. 2516-2524
    • Sorin, E.J.1    Rhee, Y.M.2    Pande, V.S.3
  • 73
    • 80052820313 scopus 로고    scopus 로고
    • Refinement of the Cornell et al. nucleic acids force field based on reference quantum chemical calculations of glycosidic torsion profiles
    • Zgarbová, M.; Otyepka, M.; Šponer, J. i.; Mládek, A. t.; Banáš, P.; Cheatham, T. E., III; Jurecka, P. Refinement of the Cornell et al. nucleic acids force field based on reference quantum chemical calculations of glycosidic torsion profiles J. Chem. Theory Comput. 2011, 7 (9) 2886-2902 10.1021/ct200162x
    • (2011) J. Chem. Theory Comput. , vol.7 , Issue.9 , pp. 2886-2902
    • Zgarbová, M.1    Otyepka, M.2    Šponer, J.I.3    Mládek, A.T.4    Banáš, P.5    Cheatham, T.E.6    Jurecka, P.7
  • 74
    • 22944441922 scopus 로고    scopus 로고
    • Incorporating variable dielectric environments into the generalized Born model
    • Sigalov, G.; Scheffel, P.; Onufriev, A. Incorporating variable dielectric environments into the generalized Born model J. Chem. Phys. 2005, 122 (9) 094511-15 10.1063/1.1857811
    • (2005) J. Chem. Phys. , vol.122 , Issue.9 , pp. 094511-094515
    • Sigalov, G.1    Scheffel, P.2    Onufriev, A.3
  • 75
    • 33748518255 scopus 로고    scopus 로고
    • Comparison of multiple Amber force fields and development of improved protein backbone parameters
    • Hornak, V.; Abel, R.; Okur, A.; Strockbine, B.; Roitberg, A.; Simmerling, C. Comparison of multiple Amber force fields and development of improved protein backbone parameters Proteins: Struct., Funct., Genet. 2006, 65 (3) 712-725 10.1002/prot.21123
    • (2006) Proteins: Struct., Funct., Genet. , vol.65 , Issue.3 , pp. 712-725
    • Hornak, V.1    Abel, R.2    Okur, A.3    Strockbine, B.4    Roitberg, A.5    Simmerling, C.6
  • 76
    • 33646940952 scopus 로고
    • Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes
    • Ryckaert, J.-P.; Ciccotti, G.; Berendsen, H. J. Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes J. Comput. Phys. 1977, 23 (3) 327-341 10.1016/0021-9991(77)90098-5
    • (1977) J. Comput. Phys. , vol.23 , Issue.3 , pp. 327-341
    • Ryckaert, J.-P.1    Ciccotti, G.2    Berendsen, H.J.3
  • 78
    • 0033468737 scopus 로고    scopus 로고
    • Application of a pairwise generalized Born model to proteins and nucleic acids: inclusion of salt effects
    • Srinivasan, J.; Trevathan, M. W.; Beroza, P.; Case, D. A. Application of a pairwise generalized Born model to proteins and nucleic acids: inclusion of salt effects Theor. Chem. Acc. 1999, 101 (6) 426-434 10.1007/s002140050460
    • (1999) Theor. Chem. Acc. , vol.101 , Issue.6 , pp. 426-434
    • Srinivasan, J.1    Trevathan, M.W.2    Beroza, P.3    Case, D.A.4
  • 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 (7) 3084-3095 10.1021/ct400341p
    • (2013) J. Chem. Theory Comput. , vol.9 , Issue.7 , pp. 3084-3095
    • Roe, D.R.1    Cheatham, T.E.2
  • 81
    • 0037423728 scopus 로고    scopus 로고
    • Structure of a G-quadruplex-Ligand Complex
    • Haider, S. M.; Parkinson, G. N.; Neidle, S. Structure of a G-quadruplex-Ligand Complex J. Mol. Biol. 2003, 326 (1) 117-125 10.1016/S0022-2836(02)01354-2
    • (2003) J. Mol. Biol. , vol.326 , Issue.1 , pp. 117-125
    • Haider, S.M.1    Parkinson, G.N.2    Neidle, S.3
  • 82
    • 0029120978 scopus 로고
    • Terminal Base-Pairs of Oligodeoxynucleotides - Imino Proton-Exchange and Fraying
    • Nonin, S.; Leroy, J. L.; Gueron, M. Terminal Base-Pairs of Oligodeoxynucleotides-Imino Proton-Exchange and Fraying Biochemistry 1995, 34 (33) 10652-10659 10.1021/bi00033a041
    • (1995) Biochemistry , vol.34 , Issue.33 , pp. 10652-10659
    • Nonin, S.1    Leroy, J.L.2    Gueron, M.3
  • 83
    • 79751535311 scopus 로고    scopus 로고
    • Improving the description of salt bridge strength and geometry in a Generalized Born model
    • Shang, Y.; Nguyen, H.; Wickstrom, L.; Okur, A.; Simmerling, C. Improving the description of salt bridge strength and geometry in a Generalized Born model J. Mol. Graphics Modell. 2011, 29 (5) 676-684 10.1016/j.jmgm.2010.11.013
    • (2011) J. Mol. Graphics Modell. , vol.29 , Issue.5 , pp. 676-684
    • Shang, Y.1    Nguyen, H.2    Wickstrom, L.3    Okur, A.4    Simmerling, C.5
  • 84
    • 84881521091 scopus 로고    scopus 로고
    • Structural dynamics of possible late-stage intermediates in folding of quadruplex DNA studied by molecular simulations
    • Stadlbauer, P.; Krepl, M.; Cheatham, T. E.; Koča, J.; Šponer, J. Structural dynamics of possible late-stage intermediates in folding of quadruplex DNA studied by molecular simulations Nucleic Acids Res. 2013, 41 (14) 7128-7143 10.1093/nar/gkt412
    • (2013) Nucleic Acids Res. , vol.41 , Issue.14 , pp. 7128-7143
    • Stadlbauer, P.1    Krepl, M.2    Cheatham, T.E.3    Koča, J.4    Šponer, J.5
  • 85
    • 33645401742 scopus 로고    scopus 로고
    • G-Quadruplexes Can Maintain Their Structure in the Gas Phase
    • Rueda, M.; Luque, F. J.; Orozco, M. G-Quadruplexes Can Maintain Their Structure in the Gas Phase J. Am. Chem. Soc. 2006, 128 (11) 3608-3619 10.1021/ja055936s
    • (2006) J. Am. Chem. Soc. , vol.128 , Issue.11 , pp. 3608-3619
    • Rueda, M.1    Luque, F.J.2    Orozco, M.3
  • 86
    • 0029941154 scopus 로고    scopus 로고
    • Observation of the A-DNA to B-DNA transition during unrestrained molecular dynamics in aqueous solution
    • Cheatham, T. E., III; Kollman, P. A. Observation of the A-DNA to B-DNA transition during unrestrained molecular dynamics in aqueous solution J. Mol. Biol. 1996, 259 (3) 434-444 10.1006/jmbi.1996.0330
    • (1996) J. Mol. Biol. , vol.259 , Issue.3 , pp. 434-444
    • Cheatham, T.E.1    Kollman, P.A.2
  • 87
    • 0033064123 scopus 로고    scopus 로고
    • Unrestrained stochastic dynamics simulations of the UUCG tetraloop using an implicit solvation model
    • Williams, D. J.; Hall, K. B. Unrestrained stochastic dynamics simulations of the UUCG tetraloop using an implicit solvation model Biophys. J. 1999, 76 (6) 3192-3205 10.1016/S0006-3495(99)77471-0
    • (1999) Biophys. J. , vol.76 , Issue.6 , pp. 3192-3205
    • Williams, D.J.1    Hall, K.B.2
  • 88
    • 20644449471 scopus 로고    scopus 로고
    • Modification of the Generalized Born Model Suitable for Macromolecules
    • Onufriev, A.; Bashford, D.; Case, D. A. Modification of the Generalized Born Model Suitable for Macromolecules J. Phys. Chem. B 2000, 104 (15) 3712-3720 10.1021/jp994072s
    • (2000) J. Phys. Chem. B , vol.104 , Issue.15 , pp. 3712-3720
    • Onufriev, A.1    Bashford, D.2    Case, D.A.3


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