메뉴 건너뛰기




Volumn 10, Issue 6, 2014, Pages 2528-2536

Resolution-adapted all-atomic and coarse-grained model for biomolecular simulations

Author keywords

[No Author keywords available]

Indexed keywords


EID: 84902146276     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/ct401029k     Document Type: Article
Times cited : (22)

References (73)
  • 3
    • 84865383775 scopus 로고    scopus 로고
    • On developing coarse-grained models for biomolecular simulation: A review
    • Riniker, S.; Allison, J. R.; van Gunsteren, W. F. On developing coarse-grained models for biomolecular simulation: A review Phys. Chem. Chem. Phys. 2012, 14, 12423
    • (2012) Phys. Chem. Chem. Phys. , vol.14 , pp. 12423
    • Riniker, S.1    Allison, J.R.2    Van Gunsteren, W.F.3
  • 5
    • 84884807653 scopus 로고    scopus 로고
    • Perspective: Coarse-grained models for biomolecular systems
    • Noid, W. G. Perspective: Coarse-grained models for biomolecular systems J. Chem. Phys. 2013, 139, 090901
    • (2013) J. Chem. Phys. , vol.139 , pp. 090901
    • Noid, W.G.1
  • 6
    • 77957897253 scopus 로고    scopus 로고
    • Recent progress in adaptive multiscale molecular dynamics simulations of soft matter
    • Nielsen, S. O.; Bulo, R. E.; Moore, P. B.; Ensing, B. Recent progress in adaptive multiscale molecular dynamics simulations of soft matter Phys. Chem. Chem. Phys. 2010, 12, 12401
    • (2010) Phys. Chem. Chem. Phys. , vol.12 , pp. 12401
    • Nielsen, S.O.1    Bulo, R.E.2    Moore, P.B.3    Ensing, B.4
  • 7
    • 84888825453 scopus 로고    scopus 로고
    • Coarse-grain modelling of protein-protein interactions
    • Baaden, M.; Marrink, S. J. Coarse-grain modelling of protein-protein interactions Curr. Opinion Struct. Biol. 2013, 23, 878
    • (2013) Curr. Opinion Struct. Biol. , vol.23 , pp. 878
    • Baaden, M.1    Marrink, S.J.2
  • 8
    • 84877743189 scopus 로고    scopus 로고
    • Coarse-graining methods for computational biology
    • Saunders, M. G.; Voth, G. A. Coarse-graining methods for computational biology Annu. Rev. Biophys. 2013, 42, 73
    • (2013) Annu. Rev. Biophys. , vol.42 , pp. 73
    • Saunders, M.G.1    Voth, G.A.2
  • 9
  • 10
    • 34548187754 scopus 로고    scopus 로고
    • From rigid base pairs to semiflexible polymers: Coarse-graining DNA
    • Becker, N. B.; Everaers, R. From rigid base pairs to semiflexible polymers: Coarse-graining DNA Phys. Rev. E 2007, 76, 021923
    • (2007) Phys. Rev. e , vol.76 , pp. 021923
    • Becker, N.B.1    Everaers, R.2
  • 11
    • 77951569390 scopus 로고    scopus 로고
    • DNA nanotweezers studied with a coarse-grained model of DNA
    • Ouldridge, T. E.; Louis, A. A.; Doye, J. P. K. DNA nanotweezers studied with a coarse-grained model of DNA Phys. Rev. Lett. 2010, 104, 178101
    • (2010) Phys. Rev. Lett. , vol.104 , pp. 178101
    • Ouldridge, T.E.1    Louis, A.A.2    Doye, J.P.K.3
  • 12
    • 80155123722 scopus 로고    scopus 로고
    • Coarse-grained model for protein folding based on structural profiles
    • Wolff, K.; Vendruscolo, M.; Porto, M. Coarse-grained model for protein folding based on structural profiles Phys. Rev. E 2011, 84, 041934
    • (2011) Phys. Rev. e , vol.84 , pp. 041934
    • Wolff, K.1    Vendruscolo, M.2    Porto, M.3
  • 13
    • 84859565600 scopus 로고    scopus 로고
    • Peptide chain dynamics in light and heavy water: Zooming in on internal friction
    • Schulz, J. C. F.; Schmidt, L.; Best, R. B.; Dzubiella, J.; Netz, R. R. Peptide chain dynamics in light and heavy water: Zooming in on internal friction J. Am. Chem. Soc. 2012, 134, 6273
    • (2012) J. Am. Chem. Soc. , vol.134 , pp. 6273
    • Schulz, J.C.F.1    Schmidt, L.2    Best, R.B.3    Dzubiella, J.4    Netz, R.R.5
  • 15
    • 84934442761 scopus 로고    scopus 로고
    • Coarse-grained models for protein folding and aggregation
    • Derreumaux, P. Coarse-grained models for protein folding and aggregation Methods Mol. Biol. 2013, 924, 585
    • (2013) Methods Mol. Biol. , vol.924 , pp. 585
    • Derreumaux, P.1
  • 16
    • 84934434274 scopus 로고    scopus 로고
    • Multiscale molecular dynamics simulations of membrane proteins
    • Khalid, S.; Bond, P. J. Multiscale molecular dynamics simulations of membrane proteins Methods Mol. Biol. 2013, 924, 635
    • (2013) Methods Mol. Biol. , vol.924 , pp. 635
    • Khalid, S.1    Bond, P.J.2
  • 18
    • 84885143685 scopus 로고    scopus 로고
    • Allosteric activation transitions in enzymes and biomolecular motors: Insights from atomistic and coarse-grained simulations
    • Klinman, J. Hammes-Schiffer, S. Springer: New York, Vol.
    • Daily, M. D.; Yu, H.; Phillips, G. N., Jr.; Cui, Q., Allosteric activation transitions in enzymes and biomolecular motors: Insights from atomistic and coarse-grained simulations. In Dynamics in Enzyme Catalysis; Klinman, J.; Hammes-Schiffer, S., Eds.; Springer: New York, 2013; Vol. 337, pp 139.
    • (2013) Dynamics in Enzyme Catalysis , vol.337 , pp. 139
    • Daily, M.D.1    Yu, H.2    Phillips Jr., G.N.3    Cui, Q.4
  • 19
    • 84893369497 scopus 로고    scopus 로고
    • Theoretical frameworks for multiscale modeling and simulation
    • Zhou, H.-X. Theoretical frameworks for multiscale modeling and simulation Curr. Opinion Struct. Biol. 2014, 25, 67
    • (2014) Curr. Opinion Struct. Biol. , vol.25 , pp. 67
    • Zhou, H.-X.1
  • 21
    • 79954524314 scopus 로고    scopus 로고
    • From coarse grained to atomistic: A serial multiscale approach to membrane protein simulations
    • Stansfeld, P. J.; Sansom, M. S. P. From coarse grained to atomistic: A serial multiscale approach to membrane protein simulations J. Chem. Theory Comput. 2011, 7, 1157
    • (2011) J. Chem. Theory Comput. , vol.7 , pp. 1157
    • Stansfeld, P.J.1    Sansom, M.S.P.2
  • 22
    • 34547926023 scopus 로고    scopus 로고
    • Multigraining: An algorithm for simultaneous fine-grained and coarse-grained simulation of molecular systems
    • Christen, M.; Gunsteren, W. F. v. Multigraining: An algorithm for simultaneous fine-grained and coarse-grained simulation of molecular systems J. Chem. Phys. 2006, 124, 154106
    • (2006) J. Chem. Phys. , vol.124 , pp. 154106
    • Christen, M.1    Gunsteren, W.F.V.2
  • 24
    • 52649162293 scopus 로고    scopus 로고
    • Reconstructing atomistic detail for coarse-grained models with resolution exchange
    • Liu, P.; Shi, Q.; Lyman, E.; Voth, G. A. Reconstructing atomistic detail for coarse-grained models with resolution exchange J. Chem. Phys. 2008, 129, 114103
    • (2008) J. Chem. Phys. , vol.129 , pp. 114103
    • Liu, P.1    Shi, Q.2    Lyman, E.3    Voth, G.A.4
  • 25
    • 78650341784 scopus 로고    scopus 로고
    • Scalable free energy calculation of proteins via multiscale essential sampling
    • Moritsugu, K.; Terada, T.; Kidera, A. Scalable free energy calculation of proteins via multiscale essential sampling J. Chem. Phys. 2010, 133, 224105
    • (2010) J. Chem. Phys. , vol.133 , pp. 224105
    • Moritsugu, K.1    Terada, T.2    Kidera, A.3
  • 26
    • 79751533108 scopus 로고    scopus 로고
    • Multi-scale free energy landscape calculation method by combination of coarse-grained and all-atom models
    • Harada, R.; Kitao, A. Multi-scale free energy landscape calculation method by combination of coarse-grained and all-atom models Chem. Phys. Lett. 2011, 503, 145
    • (2011) Chem. Phys. Lett. , vol.503 , pp. 145
    • Harada, R.1    Kitao, A.2
  • 27
    • 29144483372 scopus 로고    scopus 로고
    • Adaptive resolution molecular-dynamics simulation: Changing the degrees of freedom on the fly
    • Praprotnik, M.; Site, L. D.; Kremer, K. Adaptive resolution molecular-dynamics simulation: Changing the degrees of freedom on the fly J. Chem. Phys. 2005, 123, 224106
    • (2005) J. Chem. Phys. , vol.123 , pp. 224106
    • Praprotnik, M.1    Site, L.D.2    Kremer, K.3
  • 29
    • 73949137758 scopus 로고    scopus 로고
    • Mixed resolution modeling of interactions in condensed-phase systems
    • Izvekov, S.; Voth, G. A. Mixed resolution modeling of interactions in condensed-phase systems J. Chem. Theory Comput. 2009, 5, 3232
    • (2009) J. Chem. Theory Comput. , vol.5 , pp. 3232
    • Izvekov, S.1    Voth, G.A.2
  • 30
    • 73149092783 scopus 로고    scopus 로고
    • Solving the equations of motion for mixed atomistic and coarse-grained systems
    • Park, J. H.; Heyden, A. Solving the equations of motion for mixed atomistic and coarse-grained systems Mol. Sim. 2009, 35, 962
    • (2009) Mol. Sim. , vol.35 , pp. 962
    • Park, J.H.1    Heyden, A.2
  • 32
    • 79959749835 scopus 로고    scopus 로고
    • Hybrid simulations: Combining atomistic and coarse-grained force fields using virtual sites
    • Rzepiela, A. J.; Louhivuori, M.; Peter, C.; Marrink, S. J. Hybrid simulations: Combining atomistic and coarse-grained force fields using virtual sites Phys. Chem. Chem. Phys. 2011, 13, 10437
    • (2011) Phys. Chem. Chem. Phys. , vol.13 , pp. 10437
    • Rzepiela, A.J.1    Louhivuori, M.2    Peter, C.3    Marrink, S.J.4
  • 33
    • 84866529267 scopus 로고    scopus 로고
    • Solvating atomic level fine-grained proteins in supra-molecular level coarse-grained water for molecular dynamics simulations
    • Riniker, S.; Eichenberger, A.; van Gunsteren, W. Solvating atomic level fine-grained proteins in supra-molecular level coarse-grained water for molecular dynamics simulations Eur. Biophys. J. 2012, 41, 647
    • (2012) Eur. Biophys. J. , vol.41 , pp. 647
    • Riniker, S.1    Eichenberger, A.2    Van Gunsteren, W.3
  • 34
    • 84864755959 scopus 로고    scopus 로고
    • Structural effects of an atomic-level layer of water molecules around proteins solvated in supra-molecular coarse-grained water
    • Riniker, S.; Eichenberger, A. P.; van Gunsteren, W. F. Structural effects of an atomic-level layer of water molecules around proteins solvated in supra-molecular coarse-grained water J. Phys. Chem. B 2012, 116, 8873
    • (2012) J. Phys. Chem. B , vol.116 , pp. 8873
    • Riniker, S.1    Eichenberger, A.P.2    Van Gunsteren, W.F.3
  • 35
    • 84871675526 scopus 로고    scopus 로고
    • Mixing coarse-grained and fine-grained water in molecular dynamics simulations of a single system
    • Riniker, S.; van Gunsteren, W. F. Mixing coarse-grained and fine-grained water in molecular dynamics simulations of a single system J. Chem. Phys. 2012, 137, 044120
    • (2012) J. Chem. Phys. , vol.137 , pp. 044120
    • Riniker, S.1    Van Gunsteren, W.F.2
  • 36
    • 84875777145 scopus 로고    scopus 로고
    • Mixing MARTINI: Electrostatic coupling in hybrid atomistic-coarse-grained biomolecular simulations
    • Wassenaar, T. A.; Ingólfsson, H. I.; Prieß, M.; Marrink, S. J.; Schäfer, L. V. Mixing MARTINI: electrostatic coupling in hybrid atomistic-coarse-grained biomolecular simulations J. Phys. Chem. B 2013, 117, 3516
    • (2013) J. Phys. Chem. B , vol.117 , pp. 3516
    • Wassenaar, T.A.1    Ingólfsson, H.I.2    Prieß, M.3    Marrink, S.J.4    Schäfer, L.V.5
  • 37
    • 0017100947 scopus 로고
    • Theoretical studies of enzymic reactions: Dielectric, electrostatic, and steric stabilization of the carbonium ion in the reaction of lysozyme
    • Warshel, A.; Levitt, M. Theoretical studies of enzymic reactions: Dielectric, electrostatic, and steric stabilization of the carbonium ion in the reaction of lysozyme J. Mol. Biol. 1976, 103, 227
    • (1976) J. Mol. Biol. , vol.103 , pp. 227
    • Warshel, A.1    Levitt, M.2
  • 38
    • 84986466995 scopus 로고
    • Microscopic models for quantum mechanical calculations of chemical processes in solutions: LD/AMPAC and SCAAS/AMPAC calculations of solvation energies
    • Luzhkov, V.; Warshel, A. Microscopic models for quantum mechanical calculations of chemical processes in solutions: LD/AMPAC and SCAAS/AMPAC calculations of solvation energies J. Comput. Chem. 1992, 13, 199
    • (1992) J. Comput. Chem. , vol.13 , pp. 199
    • Luzhkov, V.1    Warshel, A.2
  • 39
    • 0031187388 scopus 로고    scopus 로고
    • Langevin dipoles model for ab initio calculations of chemical processes in solution: Parametrization and application to hydration free energies of neutral and ionic solutes and conformational analysis in aqueous solution
    • Florián, J.; Warshel, A. Langevin dipoles model for ab initio calculations of chemical processes in solution: Parametrization and application to hydration free energies of neutral and ionic solutes and conformational analysis in aqueous solution J. Phys. Chem. B 1997, 101, 5583
    • (1997) J. Phys. Chem. B , vol.101 , pp. 5583
    • Florián, J.1    Warshel, A.2
  • 40
    • 0000396658 scopus 로고
    • A fast algorithm for particle simulations
    • Greengard, L.; Rokhlin, V. A fast algorithm for particle simulations J. Comput. Phys. 1987, 73, 325
    • (1987) J. Comput. Phys. , vol.73 , pp. 325
    • Greengard, L.1    Rokhlin, V.2
  • 42
    • 36649024127 scopus 로고    scopus 로고
    • Coarse-grained protein model coupled with a coarse-grained water model: Molecular dynamics study of polyalanine-based peptides
    • Han, W.; Wu, Y.-D. Coarse-grained protein model coupled with a coarse-grained water model: Molecular dynamics study of polyalanine-based peptides J. Chem. Theory Comput. 2007, 3, 2146
    • (2007) J. Chem. Theory Comput. , vol.3 , pp. 2146
    • Han, W.1    Wu, Y.-D.2
  • 44
    • 0000095892 scopus 로고    scopus 로고
    • A united-residue force field for off-lattice protein-structure simulations. I. Functional forms and parameters of long-range side-chain interaction potentials from protein crystal data
    • Liwo, A.; Ołdziej, S.; Pincus, M. R.; Wawak, R. J.; Rackovsky, S.; Scheraga, H. A. A united-residue force field for off-lattice protein-structure simulations. I. Functional forms and parameters of long-range side-chain interaction potentials from protein crystal data J. Comput. Chem. 1997, 18, 849
    • (1997) J. Comput. Chem. , vol.18 , pp. 849
    • Liwo, A.1    Ołdziej, S.2    Pincus, M.R.3    Wawak, R.J.4    Rackovsky, S.5    Scheraga, H.A.6
  • 45
    • 0000095890 scopus 로고    scopus 로고
    • A united-residue force field for off-lattice protein-structure simulations. II. Parameterization of short-range interactions and determination of weights of energy terms by Z-score optimization
    • Liwo, A.; Pincus, M. R.; Wawak, R. J.; Rackovsky, S.; Ołdziej, S.; Scheraga, H. A. A united-residue force field for off-lattice protein-structure simulations. II. Parameterization of short-range interactions and determination of weights of energy terms by Z-score optimization J. Comput. Chem. 1997, 18, 874
    • (1997) J. Comput. Chem. , vol.18 , pp. 874
    • Liwo, A.1    Pincus, M.R.2    Wawak, R.J.3    Rackovsky, S.4    Ołdziej, S.5    Scheraga, H.A.6
  • 46
    • 0001181898 scopus 로고    scopus 로고
    • United-residue force field for off-lattice protein-structure simulations: III. Origin of backbone hydrogen-bonding cooperativity in united-residue potentials
    • Liwo, A.; Kaźmierkiewicz, R.; Czaplewski, C.; Groth, M.; Ołdziej, S.; Wawak, R. J.; Rackovsky, S.; Pincus, M. R.; Scheraga, H. A. United-residue force field for off-lattice protein-structure simulations: III. Origin of backbone hydrogen-bonding cooperativity in united-residue potentials J. Comput. Chem. 1998, 19, 259
    • (1998) J. Comput. Chem. , vol.19 , pp. 259
    • Liwo, A.1    Kaźmierkiewicz, R.2    Czaplewski, C.3    Groth, M.4    Ołdziej, S.5    Wawak, R.J.6    Rackovsky, S.7    Pincus, M.R.8    Scheraga, H.A.9
  • 47
    • 84943200457 scopus 로고
    • A leap-frog algorithm for stochastic dynamics
    • Van Gunsteren, W. F.; Berendsen, H. J. C. A leap-frog algorithm for stochastic dynamics Mol. Sim. 1988, 1, 173
    • (1988) Mol. Sim. , vol.1 , pp. 173
    • Van Gunsteren, W.F.1    Berendsen, H.J.C.2
  • 48
    • 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, 1990
    • (1992) J. Chem. Phys. , vol.97 , pp. 1990
    • Tuckerman, M.1    Berne, B.J.2    Martyna, G.J.3
  • 50
    • 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, 1400
    • (2004) J. Comput. Chem. , vol.25 , pp. 1400
    • Mackerell, A.D.1    Feig, M.2    Brooks, C.L.3
  • 51
    • 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, 6127
    • (1990) J. Am. Chem. Soc. , vol.112 , pp. 6127
    • Still, W.C.1    Tempczyk, A.2    Hawley, R.C.3    Hendrickson, T.4
  • 52
    • 4043171970 scopus 로고    scopus 로고
    • The GB/SA continuum model for solvation: A fast analytical method for the calculation of approximate Born radii
    • Qiu, D.; Shenkin, P. S.; Hollinger, F. P.; Still, W. C. The GB/SA continuum model for solvation: A fast analytical method for the calculation of approximate Born radii J. Phys. Chem. A 1997, 101, 3005
    • (1997) J. Phys. Chem. A , vol.101 , pp. 3005
    • Qiu, D.1    Shenkin, P.S.2    Hollinger, F.P.3    Still, W.C.4
  • 53
    • 0032484151 scopus 로고    scopus 로고
    • Solution conformations and thermodynamics of structured peptides: Molecular dynamics simulation with an implicit solvation model
    • Schaefer, M.; Bartels, C.; Karplus, M. Solution conformations and thermodynamics of structured peptides: molecular dynamics simulation with an implicit solvation model J. Mol. Biol. 1998, 284, 835
    • (1998) J. Mol. Biol. , vol.284 , pp. 835
    • Schaefer, M.1    Bartels, C.2    Karplus, M.3
  • 54
    • 1642485164 scopus 로고    scopus 로고
    • Coarse grained model for semiquantitative lipid simulations
    • Marrink, S. J.; de Vries, A. H.; Mark, A. E. Coarse grained model for semiquantitative lipid simulations J. Phys. Chem. B 2003, 108, 750
    • (2003) J. Phys. Chem. B , vol.108 , pp. 750
    • Marrink, S.J.1    De Vries, A.H.2    Mark, A.E.3
  • 59
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
    • Kabsch, W.; Sander, C. Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features Biopolymers 1983, 22, 2577
    • (1983) Biopolymers , vol.22 , pp. 2577
    • Kabsch, W.1    Sander, C.2
  • 60
    • 84865088597 scopus 로고    scopus 로고
    • Comparison of secondary structure formation using 10 different force fields in microsecond molecular dynamics simulations
    • Cino, E. A.; Choy, W. Y.; Karttunen, M. Comparison of secondary structure formation using 10 different force fields in microsecond molecular dynamics simulations J. Chem. Theory Comput. 2012, 8, 2725
    • (2012) J. Chem. Theory Comput. , vol.8 , pp. 2725
    • Cino, E.A.1    Choy, W.Y.2    Karttunen, M.3
  • 61
    • 80053373102 scopus 로고    scopus 로고
    • Three force fields' views of the 3(10) helix
    • Patapati, K. K.; Glykos, N. M. Three force fields' views of the 3(10) helix Biophys. J. 2011, 101, 1766
    • (2011) Biophys. J. , vol.101 , pp. 1766
    • Patapati, K.K.1    Glykos, N.M.2
  • 62
    • 0035850758 scopus 로고    scopus 로고
    • β-Hairpin folding simulations in atomistic detail using an implicit solvent model
    • Zagrovic, B.; Sorin, E. J.; Pande, V. β-Hairpin folding simulations in atomistic detail using an implicit solvent model J. Mol. Biol. 2001, 313, 151
    • (2001) J. Mol. Biol. , vol.313 , pp. 151
    • Zagrovic, B.1    Sorin, E.J.2    Pande, V.3
  • 63
    • 33645078713 scopus 로고
    • Calculation of effective interaction potentials from radial distribution functions: A reverse Monte Carlo approach
    • Lyubartsev, A. P.; Laaksonen, A. Calculation of effective interaction potentials from radial distribution functions: A reverse Monte Carlo approach Phys. Rev. E 1995, 52, 3730
    • (1995) Phys. Rev. e , vol.52 , pp. 3730
    • Lyubartsev, A.P.1    Laaksonen, A.2
  • 64
    • 26844470089 scopus 로고    scopus 로고
    • Mapping atomistic simulations to mesoscopic models: A systematic coarse-graining procedure for vinyl polymer chains
    • Milano, G.; Müller-Plathe, F. Mapping atomistic simulations to mesoscopic models: A systematic coarse-graining procedure for vinyl polymer chains J. Phys. Chem. B 2005, 109, 18609
    • (2005) J. Phys. Chem. B , vol.109 , pp. 18609
    • Milano, G.1    Müller-Plathe, F.2
  • 65
    • 0042783950 scopus 로고    scopus 로고
    • Deriving effective mesoscale potentials from atomistic simulations
    • Reith, D.; Putz, M.; Muller-Plathe, F. Deriving effective mesoscale potentials from atomistic simulations J. Comput. Chem. 2003, 24, 1624
    • (2003) J. Comput. Chem. , vol.24 , pp. 1624
    • Reith, D.1    Putz, M.2    Muller-Plathe, F.3
  • 66
    • 84861169079 scopus 로고    scopus 로고
    • Liquid water simulations with the density fragment interaction approach
    • Hu, X.; Jin, Y.; Zeng, X.; Hu, H.; Yang, W. Liquid water simulations with the density fragment interaction approach Phys. Chem. Chem. Phys. 2012, 14, 7700
    • (2012) Phys. Chem. Chem. Phys. , vol.14 , pp. 7700
    • Hu, X.1    Jin, Y.2    Zeng, X.3    Hu, H.4    Yang, W.5
  • 67
    • 84861571675 scopus 로고    scopus 로고
    • DCMB that combines divide-and-conquer and mixed-basis set methods for accurate geometry optimizations, total energies, and vibrational frequencies of large molecules
    • Wu, A.; Xu, X. DCMB that combines divide-and-conquer and mixed-basis set methods for accurate geometry optimizations, total energies, and vibrational frequencies of large molecules J. Comput. Chem. 2012, 33, 1421
    • (2012) J. Comput. Chem. , vol.33 , pp. 1421
    • Wu, A.1    Xu, X.2
  • 69
    • 84884901812 scopus 로고    scopus 로고
    • Contributions of Pauli repulsions to the energetics and physical properties computed in QM/MM methods
    • Jin, Y.; Johnson, E. R.; Hu, X.; Yang, W.; Hu, H. Contributions of Pauli repulsions to the energetics and physical properties computed in QM/MM methods J. Comput. Chem. 2013, 34, 2380
    • (2013) J. Comput. Chem. , vol.34 , pp. 2380
    • Jin, Y.1    Johnson, E.R.2    Hu, X.3    Yang, W.4    Hu, H.5
  • 70
    • 46149099398 scopus 로고    scopus 로고
    • The multiscale coarse-graining method. II. Numerical implementation for coarse-grained molecular models
    • Noid, W. G.; Liu, P.; Wang, Y.; Chu, J.-W.; Ayton, G. S.; Izvekov, S.; Andersen, H. C.; Voth, G. A. The multiscale coarse-graining method. II. Numerical implementation for coarse-grained molecular models J. Chem. Phys. 2008, 128, 244115
    • (2008) J. Chem. Phys. , vol.128 , pp. 244115
    • Noid, W.G.1    Liu, P.2    Wang, Y.3    Chu, J.-W.4    Ayton, G.S.5    Izvekov, S.6    Andersen, H.C.7    Voth, G.A.8
  • 72
    • 84892157404 scopus 로고    scopus 로고
    • Classical electrostatics for biomolecular simulations
    • Cisneros, G. A.; Karttunen, M.; Ren, P. Y.; Sagui, C. Classical electrostatics for biomolecular simulations Chem. Rev. 2014, 114, 779
    • (2014) Chem. Rev. , vol.114 , pp. 779
    • Cisneros, G.A.1    Karttunen, M.2    Ren, P.Y.3    Sagui, C.4
  • 73
    • 0033024177 scopus 로고    scopus 로고
    • Molecular dynamics simulations of biomolecules: Long-range electrostatic effects
    • Sagui, C.; Darden, T. A. Molecular dynamics simulations of biomolecules: Long-range electrostatic effects Annu. Rev. Biophys. Biomol. Struct. 1999, 28, 155
    • (1999) Annu. Rev. Biophys. Biomol. Struct. , vol.28 , pp. 155
    • Sagui, C.1    Darden, T.A.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.