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Volumn 43, Issue 2, 2010, Pages 220-230

Multiscale modeling of proteins

Author keywords

[No Author keywords available]

Indexed keywords

GREEN FLUORESCENT PROTEIN; INTEGRASE; P16 PROTEASE, HUMAN IMMUNODEFICIENCY VIRUS 1; PROTEINASE;

EID: 77249151455     PISSN: 00014842     EISSN: 15204898     Source Type: Journal    
DOI: 10.1021/ar9001476     Document Type: Article
Times cited : (120)

References (75)
  • 2
    • 33947421578 scopus 로고    scopus 로고
    • Emerging methods for multiscale simulation of biomolecular systems
    • Chu, J. W.; Ayton, G. S.; Izvekov, S.; Voth, G. A. Emerging methods for multiscale simulation of biomolecular systems. Mol. Phys. 2007, 105, 167-174.
    • (2007) Mol. Phys. , vol.105 , pp. 167-174
    • Chu, J.W.1    Ayton, G.S.2    Izvekov, S.3    Voth, G.A.4
  • 3
    • 77249089645 scopus 로고    scopus 로고
    • Challenges and perspectives in biomolecular simulations: From the atomistic picture to multiscale modeling
    • Cascella, M.; Peraro, M. D. Challenges and perspectives in biomolecular simulations: From the atomistic picture to multiscale modeling. Curr. Opin. Struct. Biol. 2008, 18, 630-640.
    • (2008) Curr. Opin. Struct. Biol. , vol.18 , pp. 630-640
    • Cascella, M.1    Peraro, M.D.2
  • 5
    • 34247098754 scopus 로고    scopus 로고
    • Multiscale modeling of biomolecular systems: In serial and in parallel
    • Ayton, G. S.; Noid, W. G.; Voth, G. A. Multiscale modeling of biomolecular systems: In serial and in parallel. Curr. Opin. Struct Biol. 2007, 17, 192-198.
    • (2007) Curr. Opin. Struct Biol. , vol.17 , pp. 192-198
    • Ayton, G.S.1    Noid, W.G.2    Voth, G.A.3
  • 6
    • 34548576414 scopus 로고
    • Purification and properties of aequorin, a bioluminescent protein from the luminous hydromedusan, Aequorea
    • Shimomura, O.; Johnson, F. H.; Saiga, Y. J. Extraction, purification and properties of aequorin, a bioluminescent protein from the luminous hydromedusan, Aequorea. J. Cell. Comp. Physiol. 1962, 59, 223-239.
    • (1962) J. Cell. Comp. Physiol. , vol.59 , pp. 223-239
    • Shimomura, O.1    Johnson, F.H.2    Extraction, S.Y.J.3
  • 7
    • 23444431611 scopus 로고
    • Green fluorescent protein as a marker for gene expression
    • Chalfie, M.; Tu, Y.; Euskirchen, G.; Ward, W.; Prasher, D. Green fluorescent protein as a marker for gene expression. Science 1994, 263, 802-805 (Pubitemid 24093206)
    • (1994) Science , vol.263 , Issue.5148 , pp. 802-805
    • Chalfie, M.1    Tu, Y.2    Euskirchen, G.3    Ward, W.W.4    Prasher, D.C.5
  • 8
    • 0031663369 scopus 로고    scopus 로고
    • Green fluorescent protein
    • Tsien, R. Green fluorescent protein. Annu. Rev. Biochem. 1998, 67, 509-544
    • (1998) Annu. Rev. Biochem. , vol.67 , pp. 509-544
    • Tsien, R.1
  • 10
    • 0041922335 scopus 로고    scopus 로고
    • HIV-1 protease inhibitors: A comparative QSAR analysis
    • DOI 10.2174/0929867033457070
    • Kurup, A.; Mekapati, S.; Garg, R.; Hansch, C. HIV-1 protease Inhibitors: A comparative QSAR analysis. Curr. Med. Chem. 2003, 10, 1679-1688. (Pubitemid 37038593)
    • (2003) Current Medicinal Chemistry , vol.10 , Issue.17 , pp. 1679-1688
    • Kurup, A.1    Mekapati, S.B.2    Garg, R.3    Hansch, C.4
  • 11
    • 0000323669 scopus 로고    scopus 로고
    • Ab initio molecular dynamics: Theory and implementation
    • Grotendorst, J., Ed.; John von Neumann Institute for Computing: Jülich, Germany
    • Marx, D.; Hutter, J. Ab initio molecular dynamics: Theory and Implementation, Grotendorst, J., Ed.; NIC Series, Vol 1; John von Neumann Institute for Computing: Jülich, Germany, 2000.
    • (2000) NIC Series , vol.1
    • Marx, D.1    Hutter, J.2
  • 12
    • 0038034635 scopus 로고    scopus 로고
    • Ab initio methods for electron correlation in molecules
    • Grotendorst, J., 2nd Ed. Ed.; John von Neumann Institute for Computing: Jülich, Germany
    • Knowles, P.; Schütz, M.; Werner, H.-J. Ab Initio Methods for Electron Correlation in Molecules; Modern Methods and Algorithms of Quantum Chemistry, Proceedings, 2nd ed.; Grotendorst, J., Ed.; John von Neumann Institute for Computing: Jülich, Germany, 2000.
    • (2000) Modern Methods and Algorithms of Quantum Chemistry, Proceedings
    • Knowles, P.1    Schütz, M.2    Werner, H.-J.3
  • 13
    • 3342927029 scopus 로고    scopus 로고
    • Time-dependent density functional theory
    • Marques, M.; Gross, E. Time-dependent density functional theory. Annu. Rev. Phys. Chem. 2004, 55, 427-455.
    • (2004) Annu. Rev. Phys. Chem. , vol.55 , pp. 427-455
    • Marques, M.1    Gross, E.2
  • 14
    • 0242443693 scopus 로고    scopus 로고
    • Force fields for protein simulations
    • Ponder, J. W.; Case, D. A. Force fields for protein simulations. Adv. Protein Chem. 2003, 66, 27-85.
    • (2003) Adv. Protein Chem. , vol.66 , pp. 27-85
    • Ponder, J.W.1    Case, D.A.2
  • 17
    • 34147185256 scopus 로고    scopus 로고
    • Investigating biological systems using first principles Car-Parrinollo molecular dynamics simulations
    • Peraro, M. D.; Ruggerone, P.; Raugei, S.; Gervasio, F. L; Carloni, P. Investigating biological systems using first principles Car-Parrinollo molecular dynamics simulations. Curr. Opin. Struct Biol. 2007, 17, 149-156.
    • (2007) Curr. Opin. Struct Biol. , vol.17 , pp. 149-156
    • Peraro, M.D.1    Ruggerone, P.2    Raugei, S.3    Gervasio, F.L.4    Carloni, P.5
  • 18
    • 63849294621 scopus 로고    scopus 로고
    • Identification of two distinct inactive conformations of the β2-adrenergic receptor reconciles structural and biochemical observations
    • Dror, R. O.; Arlow, D. H.; Borhani, D. W.; Jensen, M.; Piana, S.; Shaw, D. E. Identification of two distinct inactive conformations of the β2-adrenergic receptor reconciles structural and biochemical observations. Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 4689-4694.
    • (2009) Proc. Natl. Acad. Sci. U.S.A. , vol.106 , pp. 4689-4694
    • Dror, R.O.1    Arlow, D.H.2    Borhani, D.W.3    Jensen, M.4    Piana, S.5    Shaw, D.E.6
  • 19
    • 17044393884 scopus 로고    scopus 로고
    • Coarse grained models for proteins
    • Tozzini, V. Coarse grained models for proteins. Curr. Opin. Struct. Biol. 2005, 15, 144-150.
    • (2005) Curr. Opin. Struct. Biol. , vol.15 , pp. 144-150
    • Tozzini, V.1
  • 20
    • 33846213672 scopus 로고    scopus 로고
    • Mapping all-atom models onto one-bead coarse grained models: General properties and applications to a minimal polypeptide model
    • Tozzini, V.; Rocchia, W.; McCammon, J. A. Mapping all-atom models onto one-bead coarse grained models: General properties and applications to a minimal polypeptide model. J. Chem. Theory Comput 2006, 2, 667-673.
    • (2006) J. Chem. Theory Comput , vol.2 , pp. 667-673
    • Tozzini, V.1    Rocchia, W.2    McCammon, J.A.3
  • 21
    • 0042783950 scopus 로고    scopus 로고
    • Deriving effective mesoscale potentials from atomistic simulations
    • Reith, D.; Puetz, M.; Mueller-Plathe, F. Deriving effective mesoscale potentials from atomistic simulations. J. Comput. Chem. 2003, 24, 1264-1275.
    • (2003) J. Comput. Chem. , vol.24 , pp. 1264-1275
    • Reith, D.1    Puetz, M.2    Mueller-Plathe, F.3
  • 22
    • 46149109506 scopus 로고    scopus 로고
    • The multiscale coarse-graining method I: A rigorous bridge between atomistic and coarse-grained models
    • Noid, W. G.; Chu, J. W.; Ayton, G. S.; Krishna, V.; Izvekov, S.; Voth, G. A.; Das, A.; Andersen, H. C. The multiscale coarse-graining method I: A rigorous bridge between atomistic and coarse-grained models. J. Chem. Phys. 2008, 128, 244114.
    • (2008) J. Chem. Phys. , vol.128 , pp. 244114
    • Noid, W.G.1    Chu, J.W.2    Ayton, G.S.3    Krishna, V.4    Izvekov, S.5    Voth, G.A.6    Das, A.7    Andersen, H.C.8
  • 24
    • 61449160619 scopus 로고    scopus 로고
    • Coarse-grained models reveal functional dynamics. I. Elastic network models-theories, comparisons and perspectives
    • (a) Yang, L.-W.; Chng, C.-P. Coarse-grained models reveal functional dynamics. I. Elastic network models-theories, comparisons and perspectives. Bioinf. Biol. Insights 2008, 2, 25-45.
    • (2008) Bioinf. Biol. Insights , vol.2 , pp. 25-45
    • Yang, L.-W.1    Chng, C.-P.2
  • 25
    • 24144478280 scopus 로고    scopus 로고
    • Exploring global motions and correlations in the ribosome
    • (b) Trylska, J.; Tozzini, V.; McCammon, J. A. Exploring global motions and correlations in the ribosome. Biophys. J. 2005, 89, 1455-1463.
    • (2005) Biophys. J. , vol.89 , pp. 1455-1463
    • Trylska, J.1    Tozzini, V.2    McCammon, J.A.3
  • 26
    • 24644483073 scopus 로고    scopus 로고
    • Large amplitude conformational change in proteins explored with a plastic network model: Adenylate kinase
    • DOI 10.1016/j.jmb.2005.07.031, PII S0022283605008193
    • (c) Maragakis, P.; Karplus, M. Large amplitude conformational change in proteins explored with a plastic network model: Adenylate kinase. J. Mol. Biol. 2005, 352, 807-822. (Pubitemid 41267070)
    • (2005) Journal of Molecular Biology , vol.352 , Issue.4 , pp. 807-822
    • Maragakis, P.1    Karplus, M.2
  • 27
    • 36849057606 scopus 로고    scopus 로고
    • Coarse-grained free energy functions for studying protein conformational changes: A Double-well network model
    • (d) Chu, J.-W.; Voth, G. A. Coarse-grained free energy functions for studying protein conformational changes: A Double-well network model. Biophys. J. 2007, 93, 3860-3871.
    • (2007) Biophys. J. , vol.93 , pp. 3860-3871
    • Chu, J.-W.1    Voth, G.A.2
  • 28
    • 58149161251 scopus 로고    scopus 로고
    • Systematic multiscale parameterization of heterogeneous elastic network models of proteins
    • (e) Lyman, E.; Pfaendtner, J.; Voth, G. A. Systematic multiscale parameterization of heterogeneous elastic network models of proteins. Biophys. J. 2008, 95, 4183-4192.
    • (2008) Biophys. J. , vol.95 , pp. 4183-4192
    • Lyman, E.1    Pfaendtner, J.2    Voth, G.A.3
  • 29
    • 33846247964 scopus 로고    scopus 로고
    • Computing the amino acid specificity of fluctuations in biomolecular systems
    • (f) Hamacher, K.; McCammon, J. A. Computing the amino acid specificity of fluctuations in biomolecular systems. J. Chem. Theory Comput. 2006, 2, 873-878.
    • (2006) J. Chem. Theory Comput. , vol.2 , pp. 873-878
    • Hamacher, K.1    McCammon, J.A.2
  • 30
    • 28944434207 scopus 로고    scopus 로고
    • A connection rule for α-carbon coarse-grained elastic network models using chemical bond information
    • (g) Jeong, J. I.; Jang, Y.; Kim, M. K. A connection rule for α-carbon coarse-grained elastic network models using chemical bond information. J Mol Graphics Modell. 2005, 24, 296-306.
    • (2005) J Mol Graphics Modell. , vol.24 , pp. 296-306
    • Jeong, J.I.1    Jang, Y.2    Kim, M.K.3
  • 31
    • 0017842051 scopus 로고
    • Studies on protein folding, unfolding, and fluctuations by computer simulation. II. A three-dimensional lattice model of lysozyme
    • (h) Hueda, Y.; Taketomi, H.; Go, N. Studies on protein folding, unfolding, and fluctuations by computer simulation. II. A three-dimensional lattice model of lysozyme. Biopolymers 1987, 17, 1531-1548.
    • (1987) Biopolymers , vol.17 , pp. 1531-1548
    • Hueda, Y.1    Taketomi, H.2    Go, N.3
  • 34
    • 38549133951 scopus 로고    scopus 로고
    • A coarse-grained α-carbon protein model with anisotropic hydrogen-bonding
    • DOI 10.1002/prot.21515
    • (k) Yap, E.H.; Fawzi, N. L.; Head-Gordon, T. A coarse-grained α-carbon protein model with anisotropic hydrogen-bonding. Proteins: Struct. Funct. Bioinf. 2008, 70, 626-638. (Pubitemid 351161925)
    • (2008) Proteins: Structure, Function and Genetics , vol.70 , Issue.3 , pp. 626-638
    • Yap, E.-H.1    Fawzi, N.L.2    Head-Gordon, T.3
  • 35
    • 0034646218 scopus 로고    scopus 로고
    • Mechanisms and kinetics of β-hairpin formation
    • (l) Klimov, D.; Thimmalai, D. Mechanisms and kinetics of β-hairpin formation. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 2544-2549.
    • (2000) Proc. Natl. Acad. Sci. U.S.A. , vol.97 , pp. 2544-2549
    • Klimov, D.1    Thimmalai, D.2
  • 36
    • 0037426218 scopus 로고    scopus 로고
    • Correlation between rate of folding, energy landscape, and topology in the folding of a model protein HP-36
    • (m) Mukherjee, A.; Bagchi, B. Correlation between rate of folding, energy landscape, and topology In the folding of a model protein HP-36. J Chem Phys 2003, 118, 4733-4747.
    • (2003) J Chem Phys , vol.118 , pp. 4733-4747
    • Mukherjee, A.1    Bagchi, B.2
  • 38
    • 14044266389 scopus 로고    scopus 로고
    • Ab initio simulations of protein-folding pathways by molecular dynamics with the united-residue model of polypeptide chains
    • (o) Liwo, A.; Khalili, M.; Sheraga, H.A. Ab initio simulations of protein-folding pathways by molecular dynamics with the united-residue model of polypeptide chains. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 2362-2367.
    • (2005) Proc. Natl. Acad. Sci. U.S.A. , vol.102 , pp. 2362-2367
    • Liwo, A.1    Khalili, M.2    Sheraga, H.A.3
  • 39
    • 0029942661 scopus 로고    scopus 로고
    • Structure-derived potentials and protein simulations
    • (p) Jernigan, R.; Bahar, I. Structure-derived potentials and protein simulations. Curr. Opin. Struct. Biol. 1996, 6, 195-1109
    • (1996) Curr. Opin. Struct. Biol. , vol.6 , pp. 195-1109
    • Jernigan, R.1    Bahar, I.2
  • 40
    • 24344438610 scopus 로고    scopus 로고
    • A coarse grained model for the dynamics of flap opening in HIV-1 protease
    • DOI 10.1016/j.cplett.2005.07.075, PII S0009261405010663
    • (q) Tozzini, V.; McCammon, J. A coarse grained model for the dynamics of flap opening in HIV-1 protease. Chem Phys Lett 2005, 413, 123-128. (Pubitemid 41252378)
    • (2005) Chemical Physics Letters , vol.413 , Issue.1-3 , pp. 123-128
    • Tozzini, V.1    McCammon, J.A.2
  • 41
    • 55149087047 scopus 로고    scopus 로고
    • Peptide folding using multiscale coarse-grained models
    • (r) Thorpe, I.; Zhou, J. S.; Voth, G. A. Peptide folding using multiscale coarse-grained models. J. Phys. Chem. B 2008, 112, 13079-13090.
    • (2008) J. Phys. Chem. B , vol.112 , pp. 13079-13090
    • Thorpe, I.1    Zhou, J.S.2    Voth, G.A.3
  • 42
    • 33750181654 scopus 로고    scopus 로고
    • Modeling real dynamics in the coarse-grained representation of condensed phase systems
    • Izvekov, S.; Voth, G. A. Modeling real dynamics in the coarse-grained representation of condensed phase systems. J. Chem. Phys. 2006, 125, 151101.
    • (2006) J. Chem. Phys. , vol.125 , pp. 151101
    • Izvekov, S.1    Voth, G.A.2
  • 43
    • 41949102408 scopus 로고    scopus 로고
    • Predicting 3D structures of protein-protein complexes
    • Vakser, I. A.; Kundrotas, P. Predicting 3D structures of protein-protein complexes. Cum. Pharm. Biotechnol. 2008, 9, 57-66.
    • (2008) Cum. Pharm. Biotechnol. , vol.9 , pp. 57-66
    • Vakser, I.A.1    Kundrotas, P.2
  • 45
    • 38949141177 scopus 로고    scopus 로고
    • Review: Continuum molecular electrostatics, salt effects, and counterion binding - A review of the Poisson-Boltzmann theory and its modifications
    • DOI 10.1002/bip.20877
    • Grochowski, P.; Trylska, J. Continuum molecular electrostatics, salt effects and counterion binding - A review of the Poisson-Boltzmann theory and its modifications. Biopolymers 2008, 89, 93-113. (Pubitemid 351211641)
    • (2008) Biopolymers , vol.89 , Issue.2 , pp. 93-113
    • Grochowski, P.1    Trylska, J.2
  • 46
    • 38549152231 scopus 로고    scopus 로고
    • Conformational sampling of peptides in cellular environments
    • DOI 10.1529/biophysj.107.116236
    • Tanizaki, S.; Clifford, J.; Connelly, B. D.; Feig, M. Conformational sampling of peptides in cellular environments. Biophys. J. 2008, 94, 747-759. (Pubitemid 351162445)
    • (2008) Biophysical Journal , vol.94 , Issue.3 , pp. 747-759
    • Tanizaki, S.1    Clifford, J.2    Connelly, B.D.3    Feig, M.4
  • 47
    • 64749106745 scopus 로고    scopus 로고
    • Systematic multiscale simulation of membrane protein systems
    • Ayton, G. S.; Voth, G. A. Systematic multiscale simulation of membrane protein systems. Curr. Opin. Struct. Biol. 2009, 19, 138-144.
    • (2009) Curr. Opin. Struct. Biol. , vol.19 , pp. 138-144
    • Ayton, G.S.1    Voth, G.A.2
  • 48
    • 14544289547 scopus 로고    scopus 로고
    • Multiscale flow simulations using particles
    • DOI 10.1146/annurev.fluid.37.061903.175753
    • Koumoutsakos, P. Multiscale flow simulation using particles. Annu. Rev. Fluid Mech. 2005, 37, 457-487. (Pubitemid 40301264)
    • (2005) Annual Review of Fluid Mechanics , vol.37 , pp. 457-487
    • Koumoutsakos, P.1
  • 50
    • 84962408650 scopus 로고    scopus 로고
    • Variation of spectral, structural, and vibrational properties within the intrinsically fluorescent proteins family: A density functional study
    • DOI 10.1002/jcc.20764
    • Nifosi, R.; Amat, P.; Tozzini, V. Variation of spectral, structural and vibrational properties within the intrinsically fluorescent proteins family: A density functional study. J Comput. Chem. 2007, 28, 2366-2377. (Pubitemid 47393514)
    • (2007) Journal of Computational Chemistry , vol.28 , Issue.14 , pp. 2366-2377
    • Nifosi, R.1    Amat, P.2    Tozzini, V.3
  • 51
    • 62649096371 scopus 로고    scopus 로고
    • Variation of spectral, structural and vibrational properties within the intrinsically fluorescent proteins family: A density functional study
    • Luin, S.; Voliani, V.; Lanza, G.; Bizzarri, R.; Nifosi, R.; Amat, P.; Tozzini, V.; Serresi, M.; Beltram, F. Variation of spectral, structural and vibrational properties within the intrinsically fluorescent proteins family: A density functional study. J. Am. Chem. Soc. 2009, 131, 96-103.
    • (2009) J. Am. Chem. Soc. , vol.131 , pp. 96-103
    • Luin, S.1    Voliani, V.2    Lanza, G.3    Bizzarri, R.4    Nifosi, R.5    Amat, P.6    Tozzini, V.7    Serresi, M.8    Beltram, F.9
  • 52
    • 38149038556 scopus 로고    scopus 로고
    • Predictions of novel two-photon absorption bands in fluorescent proteins
    • Nifosi, R.; Luo, Y. Predictions of novel two-photon absorption bands in fluorescent proteins. J Phys. Chem. B 2007, 111, 14043-14050.
    • (2007) J Phys. Chem. B , vol.111 , pp. 14043-14050
    • Nifosi, R.1    Luo, Y.2
  • 53
    • 1242293051 scopus 로고    scopus 로고
    • Relationship between structure and optical properties in green fluorescent proteins: A quantum mechanical study of the chromophore environment
    • Laino, T.; Nifosì, R.; Tozzini, V. Relationship between structure and optical properties in green fluorescent proteins: A quantum mechanical study of the chromophore environment. Chem. Phys. 2004, 298, 17-28.
    • (2004) Chem. Phys. , vol.298 , pp. 17-28
    • Laino, T.1    Nifosì, R.2    Tozzini, V.3
  • 55
    • 33646074333 scopus 로고    scopus 로고
    • Cis-trans isomerization of the chromophore in the green fluorescent protein variant E2GFP: A molecular dynamics study
    • Nifosì; Tozzini, V. Cis-trans isomerization of the chromophore in the green fluorescent protein variant E2GFP: A molecular dynamics study. Chem. Phys. 2006, 323, 358-368.
    • (2006) Chem. Phys. , vol.323 , pp. 358-368
    • Nifosì, T.V.1
  • 56
    • 0038300350 scopus 로고    scopus 로고
    • Molecular dynamics simulations of enhanced green fluorescent proteins: Effects of F64L, S65T and T203Y mutations on the ground-state proton equilibria
    • Nifosì; Tozzini, V. Molecular dynamics simulations of enhanced green fluorescent proteins: Effects of F64L, S65T and T203Y mutations on the ground-state proton equilibria. Proteins 2003, 51, 378-389.
    • (2003) Proteins , vol.51 , pp. 378-389
    • Nifosì, T.V.1
  • 57
    • 33645460315 scopus 로고    scopus 로고
    • Potential energy landscape of the photoinduced multiple proton-transfer processes in the green fluorescent protein: Classical molecular dynamics and mulfconfigurational electronic structure calculations
    • Vendrai, O.; Gelabert, R.; Moreno, M.; Lluch, J. M. Potential energy landscape of the photoinduced multiple proton-transfer processes in the green fluorescent protein: Classical molecular dynamics and mulfconfigurational electronic structure calculations. J Am. Chem. Soc. 2006, 128, 3564-3574.
    • (2006) J Am. Chem. Soc. , vol.128 , pp. 3564-3574
    • Vendrai, O.1    Gelabert, R.2    Moreno, M.3    Lluch, J.M.4
  • 58
    • 34848817065 scopus 로고    scopus 로고
    • Optical absorption of a green fluorescent protein variant: Environment effect in a density functional study
    • Camilloni, C.; Provasi, D.; Tiana, G.; Broglia, R. A. Optical absorption of a green fluorescent protein variant: Environment effect in a density functional study. J. Phys. Chem. B 2007, 111, 10807-10812.
    • (2007) J. Phys. Chem. B , vol.111 , pp. 10807-10812
    • Camilloni, C.1    Provasi, D.2    Tiana, G.3    Broglia, R.A.4
  • 59
    • 33847263415 scopus 로고    scopus 로고
    • Computational study of the absorption spectra of green fluorescent protein mutants
    • Patnaik, S.; Trohalaki, S.; Naik, R.; Stone, M. O.; Pachter, R. Computational study of the absorption spectra of green fluorescent protein mutants. Biopolymers 2006, 28, 253-263.
    • (2006) Biopolymers , vol.28 , pp. 253-263
    • Patnaik, S.1    Trohalaki, S.2    Naik, R.3    Stone, M.O.4    Pachter, R.5
  • 61
    • 38049141556 scopus 로고    scopus 로고
    • Large-scale motions and electrostatic properties of furin and HIV-1 protease
    • Carnevale, V.; Rangei, S.; Micheletti, C.; Carioni, P. Large-scale motions and electrostatic properties of furin and HIV-1 protease. J. Phys. Chem. A 2007, 111, 12327-12332.
    • (2007) J. Phys. Chem. A , vol.111 , pp. 12327-12332
    • Carnevale, V.1    Rangei, S.2    Micheletti, C.3    Carioni, P.4
  • 62
    • 0035997007 scopus 로고    scopus 로고
    • Molecular dynamics simulations of the first steps of the reaction catalyzed by HIV-1 protease
    • Tryleka, J.; Bala, P.; Geller, M.; Grochowski, P. Molecular dynamics simulations of the first steps of the reaction catalyzed by HIV-1 protease. Biophys. J. 2002, 83, 794-807. (Pubitemid 34803617)
    • (2002) Biophysical Journal , vol.83 , Issue.2 , pp. 794-807
    • Trylska, J.1    Bala, P.2    Geller, M.3    Grochowski, P.4
  • 63
    • 34848820304 scopus 로고    scopus 로고
    • Molecular dynamics studies on HIV-1 protease: A comparison of the flap motions between wild type protease and the M46I/G51D double mutant
    • Lauria, A.; Ippolito, M.; Almerico, A. Molecular dynamics studies on HIV-1 protease: A comparison of the flap motions between wild type protease and the M46I/G51D double mutant. J Mol. Modell. 2007, 13, 1151-1156.
    • (2007) J Mol. Modell. , vol.13 , pp. 1151-1156
    • Lauria, A.1    Ippolito, M.2    Almerico, A.3
  • 64
    • 33744491862 scopus 로고    scopus 로고
    • Restrained molecular dynamics simulations of HIV-1 protease: The first step in validating a new target for drug design
    • DOI 10.1002/bip.20497
    • Perryman, A.; Lin, J.; McCammon, J. Restrained molecular dynamics simulations of HIV-1 protease: The first step in validating a new target for drug design. Biopolymers 2006, 82, 272-284. (Pubitemid 43798156)
    • (2006) Biopolymers , vol.82 , Issue.3 , pp. 272-284
    • Perryman, A.L.1    Lin, J.-H.2    McCammon, J.A.3
  • 66
    • 24344438610 scopus 로고    scopus 로고
    • A coarse grained model for the dynamics of flap opening in HIV-1 Protease
    • Tozzini, V.: McCammon, J. A coarse grained model for the dynamics of flap opening in HIV-1 Protease. Chem. Phys. Lett 2005, 413, 123-128.
    • (2005) Chem. Phys. Lett , vol.413 , pp. 123-128
    • Tozzini, V.1    McCammon, J.2
  • 67
    • 33847116895 scopus 로고    scopus 로고
    • Flap opening dynamics in HIV-1 protease explored with a coarse-grained model
    • Tozzini, V.; Trybka, J.; Chang, C.-E.; McCammon, J. A. Flap opening dynamics In HIV-1 protease explored with a coarse-grained model. J. Stuct. Biol. 2007, 157, 606-615.
    • (2007) J. Stuct. Biol. , vol.157 , pp. 606-615
    • Tozzini, V.1    Trybka, J.2    Chang, C.-E.3    McCammon, J.A.4
  • 68
    • 33744940504 scopus 로고    scopus 로고
    • Gated binding of llgands to HIV-1 protease: Brownlan dynamics simulations in a coarse-grained model
    • Chang, C.-E.; Shen, T.; Trylska, J.; Tozzini, V.; McCammon, J. A. Gated binding of llgands to HIV-1 protease: Brownlan dynamics simulations in a coarse-grained model. Biophys. J 2006, 90, 3880-3885.
    • (2006) Biophys. J , vol.90 , pp. 3880-3885
    • Chang, C.-E.1    Shen, T.2    Trylska, J.3    Tozzini, V.4    McCammon, J.A.5
  • 69
    • 34250380707 scopus 로고    scopus 로고
    • HIV-1 protease substrate binding and product release pathways explored with coarse-grained molecular dynamics
    • Trylska, J.; Tozzini, V.; Chang, C.-E.; McCammon, J. A. HIV-1 protease substrate binding and product release pathways explored with coarse-grained molecular dynamics. Biophys. J 2007, 92, 4179-4187.
    • (2007) Biophys. J , vol.92 , pp. 4179-4187
    • Trylska, J.1    Tozzini, V.2    Chang, C.-E.3    McCammon, J.A.4
  • 70
    • 33847126878 scopus 로고    scopus 로고
    • Binding pathways of ligands to HIV-1 protease: Coarse-grained and atomistic simulations
    • Chang, C.-E.; Trylska, J.; Tozzini, V.; McCammon, J. A. Binding pathways of ligands to HIV-1 protease: Coarse-grained and atomistic simulations. Chem. Biol. Drug Des. 2007, 69, 5-13.
    • (2007) Chem. Biol. Drug Des. , vol.69 , pp. 5-13
    • Chang, C.-E.1    Trylska, J.2    Tozzini, V.3    McCammon, J.A.4
  • 71
    • 28844494903 scopus 로고    scopus 로고
    • Coarse-grained model of proteins incorporating atomistic detail of the active site
    • Neri, M.; Ansolmi, C.; Cascella, M.; Martian, A.; Carlonil, P. Coarse-grained model of proteins incorporating atomistic detail of the active site. Phys. Rev. Lett. 2005, 95, 218102.
    • (2005) Phys. Rev. Lett. , vol.95 , pp. 218102
    • Neri, M.1    Ansolmi, C.2    Cascella, M.3    Martian, A.4    Carlonil, P.5
  • 73
    • 68149162202 scopus 로고    scopus 로고
    • Proteins complexes of HIV-1 integrase with HAT proteins: Multi-scale models, dynamics and hypotheses on allosteric site of inhibition
    • Di Fenza, A.; Rocchia, W.; Tozzini, V. Proteins complexes of HIV-1 integrase with HAT proteins: Multi-scale models, dynamics and hypotheses on allosteric site of inhibition. Proteins 2009, 76, 946-958.
    • (2009) Proteins , vol.76 , pp. 946-958
    • Di Fenza, A.1    Rocchia, W.2    Tozzini, V.3
  • 74
    • 33646536078 scopus 로고    scopus 로고
    • The influence of macromolecular crowding on HIV-1 protease molecular dynamics
    • Minh, D.; Chang, C.-E.; Trylska, J.; Tozzini, V.; McCammon, J. The influence of macromolecular crowding on HIV-1 protease molecular dynamics. J. Am. Chem. Soc. 2006, 128, 6006-6007.
    • (2006) J. Am. Chem. Soc. , vol.128 , pp. 6006-6007
    • Minh, D.1    Chang, C.-E.2    Trylska, J.3    Tozzini, V.4    McCammon, J.5
  • 75
    • 24144448719 scopus 로고    scopus 로고
    • Effects of organelle shape on fluorescence recovery after photobleaching
    • Shalzarini, I. F.; Mezzacasa, A.; Helenius, A.; Koumoutsakos, P. Effects of organelle shape on fluorescence recovery after photobleaching. Biophys. J. 2005, 89, 1482-1492.
    • (2005) Biophys. J. , vol.89 , pp. 1482-1492
    • Shalzarini, I.F.1    Mezzacasa, A.2    Helenius, A.3    Koumoutsakos, P.4


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