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Volumn 34, Issue 4, 2005, Pages 273-284

Validation of the 53A6 GROMOS force field

Author keywords

Peptide; DNA; Force field; GROMOS; Lysozyme; Molecular dynamics simulation

Indexed keywords

DNA; EGG WHITE; LYSOZYME; PEPTIDE;

EID: 21244467488     PISSN: 01757571     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00249-004-0448-6     Document Type: Article
Times cited : (443)

References (85)
  • 1
    • 0015511563 scopus 로고
    • Conformational analysis of the sugar ring in nucleosides and nucleotides. A new description using the concept of pseudorotation
    • Altona C, Sundaralingam M (1972) Conformational analysis of the sugar ring in nucleosides and nucleotides. A new description using the concept of pseudorotation. J Am Chem Soc 94:8205-8212
    • (1972) J Am Chem Soc , vol.94 , pp. 8205-8212
    • Altona, C.1    Sundaralingam, M.2
  • 2
    • 49949125902 scopus 로고
    • Conformation of non-aromatic ring compounds-XXV. Geometry and conformation of ring D in some steroids from X-ray structure determinations
    • Altona C, Geise HJ, Romers C (1968) Conformation of non-aromatic ring compounds-XXV. Geometry and conformation of ring D in some steroids from X-ray structure determinations. Tetrahedron 24:13-32
    • (1968) Tetrahedron , vol.24 , pp. 13-32
    • Altona, C.1    Geise, H.J.2    Romers, C.3
  • 3
    • 0036975364 scopus 로고    scopus 로고
    • Molecular dynamics simulations of photoactive yellow protein (PYP) in three states of its photocycle: A comparison with X-ray and NMR data and analysis of the effects of Glu46 deprotonation and mutation
    • Antes I, Thiel W, Gunsteren WF van (2002) Molecular dynamics simulations of photoactive yellow protein (PYP) in three states of its photocycle: a comparison with X-ray and NMR data and analysis of the effects of Glu46 deprotonation and mutation. Eur Biophys J 31:504-520
    • (2002) Eur Biophys J , vol.31 , pp. 504-520
    • Antes, I.1    Thiel, W.2    Van Gunsteren, W.F.3
  • 4
    • 0037231708 scopus 로고    scopus 로고
    • Assessment of the molecular dynamics structure of DNA in solution based on calculated and observed NMR NOESY volumes and dihedral angles from scalar coupling constants
    • Arthanari H, McConnell KJ, Beger R, Young MA, Beveridge DL, Bolton PH (2003) Assessment of the molecular dynamics structure of DNA in solution based on calculated and observed NMR NOESY volumes and dihedral angles from scalar coupling constants. Biopolymers 68:3-15
    • (2003) Biopolymers , vol.68 , pp. 3-15
    • Arthanari, H.1    McConnell, K.J.2    Beger, R.3    Young, M.A.4    Beveridge, D.L.5    Bolton, P.H.6
  • 5
    • 0001439567 scopus 로고
    • The structures of the monoclinic and orthorhombic forms of hen egg-white lysozyme at 6 Å resolution
    • Artymiuk PJ, Blake CCF, Rice DW, Wilson KS (1982) The structures of the monoclinic and orthorhombic forms of hen egg-white lysozyme at 6 Å resolution. Acta Cryst B38:778-783
    • (1982) Acta Cryst , vol.B38 , pp. 778-783
    • Artymiuk, P.J.1    Blake, C.C.F.2    Rice, D.W.3    Wilson, K.S.4
  • 6
    • 0036306105 scopus 로고    scopus 로고
    • Simulations of apo- and holo-fatty acid binding protein: Structure and dynamics of protein, ligand and internal water
    • Bakowies D, Gunsteren WF van (2002) Simulations of apo- and holo-fatty acid binding protein: structure and dynamics of protein, ligand and internal water. J Mol Biol 315:713-736
    • (2002) J Mol Biol , vol.315 , pp. 713-736
    • Bakowies, D.1    Van Gunsteren, W.F.2
  • 9
    • 0032475912 scopus 로고    scopus 로고
    • Water molecules in DNA recognition II: A molecular dynamics view of the structure and hydration of the Trp operator
    • Bonvin AMJJ, Sunnerhagen M, Otting G, Gunsteren WF van (1998) Water molecules in DNA recognition II: a molecular dynamics view of the structure and hydration of the Trp operator. J Mol Biol 282:859-873
    • (1998) J Mol Biol , vol.282 , pp. 859-873
    • Bonvin, A.M.J.J.1    Sunnerhagen, M.2    Otting, G.3    Van Gunsteren, W.F.4
  • 13
    • 0036585607 scopus 로고    scopus 로고
    • A comparison of the potential energy parameters of aliphatic alkanes: Molecular dynamics simulations of triacylglycerols in the alpha phase
    • Chandrasekhar I, Gunsteren WF van (2002) A comparison of the potential energy parameters of aliphatic alkanes: molecular dynamics simulations of triacylglycerols in the alpha phase. Eur Biophys J 31:89-101
    • (2002) Eur Biophys J , vol.31 , pp. 89-101
    • Chandrasekhar, I.1    Van Gunsteren, W.F.2
  • 15
    • 0033654654 scopus 로고    scopus 로고
    • Molecular dynamics simulation of nucleic acids
    • Cheatham III TE, Kollman PA (2000) Molecular dynamics simulation of nucleic acids. Annu Rev Phys Chem 51:435-471
    • (2000) Annu Rev Phys Chem , vol.51 , pp. 435-471
    • Cheatham III, T.E.1    Kollman, P.A.2
  • 16
    • 14244271476 scopus 로고    scopus 로고
    • Molecular dynamics simulation of nucleic acids: Successes, limitations, and promise
    • Cheatham III TE, Young MA (2000) Molecular dynamics simulation of nucleic acids: successes, limitations, and promise. Biopolymers 56:232-256
    • (2000) Biopolymers , vol.56 , pp. 232-256
    • Cheatham III, T.E.1    Young, M.A.2
  • 17
    • 0026580202 scopus 로고
    • Refined solution structure and ligand-binding properties of PDC-109 domain b. A collagen-binding type II domain
    • Constantine KL, Madrid M, Bányai L, Trexler M, Patthy L, Llinás M (1992) Refined solution structure and ligand-binding properties of PDC-109 domain b. A collagen-binding type II domain. J Mol Biol 223:281-298
    • (1992) J Mol Biol , vol.223 , pp. 281-298
    • Constantine, K.L.1    Madrid, M.2    Bányai, L.3    Trexler, M.4    Patthy, L.5    Llinás, M.6
  • 19
    • 0034861838 scopus 로고    scopus 로고
    • Oligonucleotide analogues with a nucleobase-including backbone. Part 7: Molecular dynamics simulation of a DNA duplex containing a 2′- deoxyadenosine 8-(hydroxymethyl)-derived nucleotide
    • Czechtizky W, Daura X, Vasella A, Gunsteren WF van (2001) Oligonucleotide analogues with a nucleobase-including backbone. Part 7: molecular dynamics simulation of a DNA duplex containing a 2′-deoxyadenosine 8-(hydroxymethyl)-derived nucleotide. Helv Chim Acta 84:2132-2145
    • (2001) Helv Chim Acta , vol.84 , pp. 2132-2145
    • Czechtizky, W.1    Daura, X.2    Vasella, A.3    Van Gunsteren, W.F.4
  • 20
    • 0030800453 scopus 로고    scopus 로고
    • Studying the stability of a helical β-heptapeptide by molecular dynamics simulations
    • Daura X, Gunsteren WF van, Rigo D, Jaun B, Seebach D (1997) Studying the stability of a helical β-heptapeptide by molecular dynamics simulations. Chem Eur J 3:1410-1417
    • (1997) Chem Eur J , vol.3 , pp. 1410-1417
    • Daura, X.1    Van Gunsteren, W.F.2    Rigo, D.3    Jaun, B.4    Seebach, D.5
  • 21
    • 0001751804 scopus 로고    scopus 로고
    • Parametrization of aliphatic CHn united atoms of GROMOS96 force field
    • Daura X, Mark AE, Gunsteren WF van (1998) Parametrization of aliphatic CHn united atoms of GROMOS96 force field. J Comput Chem 19:535-547
    • (1998) J Comput Chem , vol.19 , pp. 535-547
    • Daura, X.1    Mark, A.E.2    Van Gunsteren, W.F.3
  • 23
    • 0033557181 scopus 로고    scopus 로고
    • Folding-unfolding thermodynamics of a β-heptapeptide from equilibrium simulations
    • Daura X, Gunsteren WF van, Mark AE (1999b) Folding-unfolding thermodynamics of a β-heptapeptide from equilibrium simulations. Proteins 34:269-280
    • (1999) Proteins , vol.34 , pp. 269-280
    • Daura, X.1    Van Gunsteren, W.F.2    Mark, A.E.3
  • 25
    • 0019387686 scopus 로고
    • Structure of a B-DNA dodecamer. 2. Influence of base sequence on helix structure
    • Dickerson RE, Drew HR (1981) Structure of a B-DNA dodecamer. 2. Influence of base sequence on helix structure. J Mol Biol 149:761-786
    • (1981) J Mol Biol , vol.149 , pp. 761-786
    • Dickerson, R.E.1    Drew, H.R.2
  • 26
    • 0019843568 scopus 로고
    • Structure of a B-DNA dodecamer. 3. Geometry of hydration
    • Drew HR, Dickerson RE (1981) Structure of a B-DNA dodecamer. 3. Geometry of hydration. J Mol Biol 151:535-556
    • (1981) J Mol Biol , vol.151 , pp. 535-556
    • Drew, H.R.1    Dickerson, R.E.2
  • 29
    • 0041819710 scopus 로고    scopus 로고
    • Relative stability of protein structures determined by X-ray crystallography or NMR spectroscopy: A molecular dynamics simulation study
    • Fan H, Mark AE (2003) Relative stability of protein structures determined by X-ray crystallography or NMR spectroscopy: a molecular dynamics simulation study. Proteins 53:111-120
    • (2003) Proteins , vol.53 , pp. 111-120
    • Fan, H.1    Mark, A.E.2
  • 30
    • 0347994106 scopus 로고    scopus 로고
    • Refinement of homology-based protein structures by molecular dynamics simulation techniques
    • Fan H, Mark AE (2004) Refinement of homology-based protein structures by molecular dynamics simulation techniques. Protein Sci 13:211-220
    • (2004) Protein Sci , vol.13 , pp. 211-220
    • Fan, H.1    Mark, A.E.2
  • 31
    • 0034499271 scopus 로고    scopus 로고
    • A new 2,2,2-trifluoroethanol model for molecular dynamics simulations
    • Fioroni M, Burger K, Mark AE, Roccatano D (2000) A new 2,2,2-trifluoroethanol model for molecular dynamics simulations. J Phys Chem B 104:12347-12354
    • (2000) J Phys Chem B , vol.104 , pp. 12347-12354
    • Fioroni, M.1    Burger, K.2    Mark, A.E.3    Roccatano, D.4
  • 32
    • 0001083043 scopus 로고    scopus 로고
    • Treatment of NOE constraints involving equivalent or nonstereoassigned protons in calculations of biomacromolecular structures
    • Fletcher CM, Jones DNM, Diamond R, Neuhaus D (1996) Treatment of NOE constraints involving equivalent or nonstereoassigned protons in calculations of biomacromolecular structures. J Biomol NMR 8:292-310
    • (1996) J Biomol NMR , vol.8 , pp. 292-310
    • Fletcher, C.M.1    Jones, D.N.M.2    Diamond, R.3    Neuhaus, D.4
  • 33
    • 0442326613 scopus 로고    scopus 로고
    • An effective force field for molecular dynamics simulations of dimethyl sulfoxide and dimethyl sulfoxide-water mixtures
    • Geerke DP, Oostenbrink C, Vegt NFA van der, Gunsteren WF van (2004) An effective force field for molecular dynamics simulations of dimethyl sulfoxide and dimethyl sulfoxide-water mixtures. J Phys Chem B 108:1436-1445
    • (2004) J Phys Chem B , vol.108 , pp. 1436-1445
    • Geerke, D.P.1    Oostenbrink, C.2    Van Der Vegt, N.F.A.3    Van Gunsteren, W.F.4
  • 34
    • 0037032269 scopus 로고    scopus 로고
    • Can one derive the conformational preference of a beta-peptide from its CD spectrum
    • Glättli A, Daura X, Seebach D, Gunsteren WF van (2002a) Can one derive the conformational preference of a beta-peptide from its CD spectrum. J Am Chem Soc 124:12972-12184
    • (2002) J Am Chem Soc , vol.124 , pp. 12972-12184
    • Glättli, A.1    Daura, X.2    Seebach, D.3    Van Gunsteren, W.F.4
  • 35
    • 0037042610 scopus 로고    scopus 로고
    • Derivation of an improved simple point charge model for liquid water: SPC/A and SPC/L
    • Glättli A, Daura X, Gunsteren WF van (2002b) Derivation of an improved simple point charge model for liquid water: SPC/A and SPC/L. J Chem Phys 116:9811-9828
    • (2002) J Chem Phys , vol.116 , pp. 9811-9828
    • Glättli, A.1    Daura, X.2    Van Gunsteren, W.F.3
  • 37
    • 0001349174 scopus 로고    scopus 로고
    • Validation of molecular dynamics simulation
    • Gunsteren WF van, Mark AE (1998) Validation of molecular dynamics simulation. J Chem Phys 108:6109-6116
    • (1998) J Chem Phys , vol.108 , pp. 6109-6116
    • Van Gunsteren, W.F.1    Mark, A.E.2
  • 40
    • 0035910479 scopus 로고    scopus 로고
    • The key to solving the protein-folding problem lies in an accurate description of the denatured state
    • Gunsteren WF van, Bürgi R, Peter C, Daura X (2001) The key to solving the protein-folding problem lies in an accurate description of the denatured state. Angew Chem Int Ed 40:351-355
    • (2001) Angew Chem Int Ed , vol.40 , pp. 351-355
    • Van Gunsteren, W.F.1    Bürgi, R.2    Peter, C.3    Daura, X.4
  • 41
    • 0031637651 scopus 로고    scopus 로고
    • Ligand binding affinity prediction by linear interaction energy methods
    • Hansson T, Marelius J, Åqvist J (1998) Ligand binding affinity prediction by linear interaction energy methods. J Comput-Aid Mol Des 12:27-35
    • (1998) J Comput-Aid Mol des , vol.12 , pp. 27-35
    • Hansson, T.1    Marelius, J.2    Åqvist, J.3
  • 42
    • 0035878765 scopus 로고    scopus 로고
    • Comparison of four methods to compute the dielectric permittivity of liquids from molecular dynamics simulations
    • Heinz TN, Gunsteren WF van, Hünenberger PH (2001) Comparison of four methods to compute the dielectric permittivity of liquids from molecular dynamics simulations. J Chem Phys 115:1125-1136
    • (2001) J Chem Phys , vol.115 , pp. 1125-1136
    • Heinz, T.N.1    Van Gunsteren, W.F.2    Hünenberger, P.H.3
  • 44
    • 33645941402 scopus 로고
    • The OPLS potential functions for proteins - Energy minimizations for crystals of cyclic peptides and crambin
    • Jorgensen WL, Tirado-Rives J (1988) The OPLS potential functions for proteins - energy minimizations for crystals of cyclic peptides and crambin. J Am Chem Soc 110:1657-1666
    • (1988) J Am Chem Soc , vol.110 , pp. 1657-1666
    • Jorgensen, W.L.1    Tirado-Rives, J.2
  • 45
    • 0029912748 scopus 로고    scopus 로고
    • Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids
    • Jorgensen WL, Maxwell DS, Tirado-Rives J (1996) Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J Am Chem Soc 118:11225-11236
    • (1996) J Am Chem Soc , vol.118 , pp. 11225-11236
    • Jorgensen, W.L.1    Maxwell, D.S.2    Tirado-Rives, J.3
  • 46
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
    • Kabsch W, Sander C (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22:2577-2637
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 47
    • 24144451813 scopus 로고    scopus 로고
    • A new GROMOS parameter set for hexapyranose-based carbohydrates
    • submitted
    • Lins RD, Hünenberger PH (2005) A new GROMOS parameter set for hexapyranose-based carbohydrates. J Comput Chem (submitted)
    • (2005) J Comput Chem
    • Lins, R.D.1    Hünenberger, P.H.2
  • 48
    • 0242396923 scopus 로고    scopus 로고
    • 3DNA: A software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures
    • Lu X-J, Olson WK (2003) 3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. Nucleic Acids Res 31:5108-5121
    • (2003) Nucleic Acids Res , vol.31 , pp. 5108-5121
    • Lu, X.-J.1    Olson, W.K.2
  • 49
    • 0142250484 scopus 로고    scopus 로고
    • Calculation of the water-cyclohexane transfer free energies of neutral amino acid side-chain analogs using the OPLS all-atom force field
    • MacCallum JL, Tieleman DP (2003) Calculation of the water-cyclohexane transfer free energies of neutral amino acid side-chain analogs using the OPLS all-atom force field. J Comput Chem 24:1930-1935
    • (2003) J Comput Chem , vol.24 , pp. 1930-1935
    • MacCallum, J.L.1    Tieleman, D.P.2
  • 50
    • 6344260593 scopus 로고
    • An all-atom empirical energy function for the simulation of nucleic-acids
    • MacKerell Jr. AD, Wiórkiewicz-Kuczera J, Karplus M (1995) An all-atom empirical energy function for the simulation of nucleic-acids. J Am Chem Soc 117:11946-11975
    • (1995) J Am Chem Soc , vol.117 , pp. 11946-11975
    • MacKerell Jr., A.D.1    Wiórkiewicz-Kuczera, J.2    Karplus, M.3
  • 52
    • 0002496235 scopus 로고    scopus 로고
    • Calculation of ligand binding free energies from molecular dynamics simulations
    • Marelius J, Hansson T, Åqvist J (1998) Calculation of ligand binding free energies from molecular dynamics simulations. Int J Quantum Chem 69:77-88
    • (1998) Int J Quantum Chem , vol.69 , pp. 77-88
    • Marelius, J.1    Hansson, T.2    Åqvist, J.3
  • 54
    • 0346458810 scopus 로고    scopus 로고
    • Free energies of binding of polychlorinated biphenyls to the estrogen receptor from a single simulation
    • Oostenbrink C, Gunsteren WF van (2004) Free energies of binding of polychlorinated biphenyls to the estrogen receptor from a single simulation. Proteins 54:237-246
    • (2004) Proteins , vol.54 , pp. 237-246
    • Oostenbrink, C.1    Van Gunsteren, W.F.2
  • 55
  • 56
    • 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 AE, Gunsteren WF van (2004) 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 25:1656-1676
    • (2004) J Comput Chem , vol.25 , pp. 1656-1676
    • Oostenbrink, C.1    Villa, A.2    Mark, A.E.3    Van Gunsteren, W.F.4
  • 57
    • 0029633186 scopus 로고
    • AMBER, a package of computer-programs for applying molecular mechanics, normal-mode analysis, molecular-dynamics and free-energy calculations to simulate the structural and energetic properties of molecules
    • Pearlman DA, Case DA, Caldwell JW, Ross WS, Cheatham III TE, DeBolt S, Ferguson D, Seibel G, Kollman PA (1995) AMBER, a package of computer-programs for applying molecular mechanics, normal-mode analysis, molecular-dynamics and free-energy calculations to simulate the structural and energetic properties of molecules. Comput Phys Comm 91:1-41
    • (1995) Comput Phys Comm , vol.91 , pp. 1-41
    • Pearlman, D.A.1    Case, D.A.2    Caldwell, J.W.3    Ross, W.S.4    Cheatham III, T.E.5    DeBolt, S.6    Ferguson, D.7    Seibel, G.8    Kollman, P.A.9
  • 58
    • 0034625927 scopus 로고    scopus 로고
    • Peptides of aminoxy acids: A molecular dynamics simulation of conformational equilibria under various conditions
    • Peter C, Daura X, Gunsteren WF van (2000) Peptides of aminoxy acids: a molecular dynamics simulation of conformational equilibria under various conditions. J Am Chem Soc 122:7461-7466
    • (2000) J Am Chem Soc , vol.122 , pp. 7461-7466
    • Peter, C.1    Daura, X.2    Van Gunsteren, W.F.3
  • 59
    • 33646940952 scopus 로고
    • Numerical integration of cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
    • Ryckaert J-P, Ciccotti G, Berendsen HJC (1977) Numerical integration of cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J Comput Phys 23:327-341
    • (1977) J Comput Phys , vol.23 , pp. 327-341
    • Ryckaert, J.-P.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 60
    • 0006161383 scopus 로고    scopus 로고
    • On the choice of dihedral angle potential energy functions for n-alkanes
    • Schuler LD, Gunsteren WF van (2000) On the choice of dihedral angle potential energy functions for n-alkanes. Mol Simulat 25:301-319
    • (2000) Mol Simulat , vol.25 , pp. 301-319
    • Schuler, L.D.1    Van Gunsteren, W.F.2
  • 61
    • 0035425883 scopus 로고    scopus 로고
    • An improved GROMOS96 force field for aliphatic hydrocarbons in the condensed phase
    • Schuler LD, Daura X, Gunsteren WF van (2001) An improved GROMOS96 force field for aliphatic hydrocarbons in the condensed phase. J Comput Chem 22:1205-1218
    • (2001) J Comput Chem , vol.22 , pp. 1205-1218
    • Schuler, L.D.1    Daura, X.2    Van Gunsteren, W.F.3
  • 64
    • 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 MR, Pitera JW, Swope WC, Pande VS (2003) Extremely precise free energy calculations of amino acid side chain analogs: Comparison of common molecular mechanics force fields for proteins. J Chem Phys 119:5740-5760
    • (2003) J Chem Phys , vol.119 , pp. 5740-5760
    • Shirts, M.R.1    Pitera, J.W.2    Swope, W.C.3    Pande, V.S.4
  • 65
    • 0032499635 scopus 로고    scopus 로고
    • The B-DNA dodecamer at high resolution reveals a spine of water on sodium
    • Shui X, McFail-Isom L, Hu GG, Dean Williams L (1998) The B-DNA dodecamer at high resolution reveals a spine of water on sodium. Biochemistry 37:8341-8355
    • (1998) Biochemistry , vol.37 , pp. 8341-8355
    • Shui, X.1    McFail-Isom, L.2    Hu, G.G.3    Dean Williams, L.4
  • 68
    • 0029162947 scopus 로고
    • Comparison of MD simulations and NMR experiments for hen lysozyme: Analysis of local fluctuations, cooperative motions and global changes
    • Smith LJ, Mark AE, Dobson CM, Gunsteren WF van (1995) Comparison of MD simulations and NMR experiments for hen lysozyme: analysis of local fluctuations, cooperative motions and global changes. Biochemistry 34:10918-10931
    • (1995) Biochemistry , vol.34 , pp. 10918-10931
    • Smith, L.J.1    Mark, A.E.2    Dobson, C.M.3    Van Gunsteren, W.F.4
  • 69
    • 0033548540 scopus 로고    scopus 로고
    • Side-chain conformational disorder in a molten globule: Molecular dynamics simulations of the A-state of human alpha-lactalbumin
    • Smith LJ, Dobson CM, Gunsteren WF van (1996) Side-chain conformational disorder in a molten globule: molecular dynamics simulations of the A-state of human alpha-lactalbumin. J Mol Biol 286:1567-1580
    • (1996) J Mol Biol , vol.286 , pp. 1567-1580
    • Smith, L.J.1    Dobson, C.M.2    Van Gunsteren, W.F.3
  • 70
    • 0033168453 scopus 로고    scopus 로고
    • Molecular dynamics simulations of human alpha-lactalbumin. Changes of the structural and dynamical properties of the protein at low pH
    • Smith LJ, Dobson CM, Gunsteren WF van (1999) Molecular dynamics simulations of human alpha-lactalbumin. Changes of the structural and dynamical properties of the protein at low pH. Proteins 36:77-86
    • (1999) Proteins , vol.36 , pp. 77-86
    • Smith, L.J.1    Dobson, C.M.2    Van Gunsteren, W.F.3
  • 71
    • 0742286773 scopus 로고    scopus 로고
    • Computer simulation of urea-water mixtures: A test of force field parameters for use in biomolecular simulation
    • Smith LJ, Berendsen HJC, Gunsteren WF van (2004) Computer simulation of urea-water mixtures: A test of force field parameters for use in biomolecular simulation. J Phys Chem A 108:1065-1071
    • (2004) J Phys Chem A , vol.108 , pp. 1065-1071
    • Smith, L.J.1    Berendsen, H.J.C.2    Van Gunsteren, W.F.3
  • 72
    • 11244289541 scopus 로고    scopus 로고
    • Validation of the GROMOS force-field parameter set 45A3 against nuclear magnetic resonance data of Hen Egg Lysozyme
    • Soares T, Daura X, Oostenbrink C, Smith LJ, van Gunsteren WF (2004) Validation of the GROMOS force-field parameter set 45A3 against nuclear magnetic resonance data of Hen Egg Lysozyme. J Biomol NMR 30:407-422
    • (2004) J Biomol NMR , vol.30 , pp. 407-422
    • Soares, T.1    Daura, X.2    Oostenbrink, C.3    Smith, L.J.4    Van Gunsteren, W.F.5
  • 74
    • 0034237485 scopus 로고    scopus 로고
    • Molecular dynamics simulation of hen egg white lysozyme: A test of the GROMOS96 force field against nuclear magnetic resonance data
    • Stocker U, Gunsteren WF van (2000) Molecular dynamics simulation of hen egg white lysozyme: a test of the GROMOS96 force field against nuclear magnetic resonance data. Proteins 40:145-153
    • (2000) Proteins , vol.40 , pp. 145-153
    • Stocker, U.1    Van Gunsteren, W.F.2
  • 75
    • 0033783932 scopus 로고    scopus 로고
    • On the similarity of properties in solution or in the crystalline state: A molecular dynamics study of hen lysozyme
    • Stocker U, Spiegel K, Gunsteren WF van (2000) On the similarity of properties in solution or in the crystalline state: a molecular dynamics study of hen lysozyme. J Biomol NMR 18:1-12
    • (2000) J Biomol NMR , vol.18 , pp. 1-12
    • Stocker, U.1    Spiegel, K.2    Van Gunsteren, W.F.3
  • 76
    • 0041854716 scopus 로고    scopus 로고
    • Understanding binding affinity: A combined isothermal titration calorimetry/molecular dynamics study of the binding of a series of hydrophobically modified benzamidinium chloride inhibitors to trypsin
    • Talhout R, Villa A, Mark AE, Engberts JBFN (2003) Understanding binding affinity: a combined isothermal titration calorimetry/molecular dynamics study of the binding of a series of hydrophobically modified benzamidinium chloride inhibitors to trypsin. J Am Chem Soc 125:10570-10579
    • (2003) J Am Chem Soc , vol.125 , pp. 10570-10579
    • Talhout, R.1    Villa, A.2    Mark, A.E.3    Engberts, J.B.F.N.4
  • 77
    • 4544369164 scopus 로고
    • A generalized reaction field method for molecular-dynamics simulations
    • Tironi IG, Sperb R, Smith PE, Gunsteren WF van (1995) A generalized reaction field method for molecular-dynamics simulations. J Chem Phys 102:5451-5459
    • (1995) J Chem Phys , vol.102 , pp. 5451-5459
    • Tironi, I.G.1    Sperb, R.2    Smith, P.E.3    Van Gunsteren, W.F.4
  • 78
    • 0034608901 scopus 로고    scopus 로고
    • The NMR structure of a DNA dodecamer in an aqueous dilute crystalline phase
    • Tjandra N, Tate S, Ono A, Kainosho M, Bax A (2000) The NMR structure of a DNA dodecamer in an aqueous dilute crystalline phase. J Am Chem Soc 122:6190-6200
    • (2000) J Am Chem Soc , vol.122 , pp. 6190-6200
    • Tjandra, N.1    Tate, S.2    Ono, A.3    Kainosho, M.4    Bax, A.5
  • 79
    • 36749110658 scopus 로고
    • Dipolar relaxation and nuclear Overhauser effects in nonrigid molecules: The effect of fluctuating internuclear distances
    • Tropp J (1980) Dipolar relaxation and nuclear Overhauser effects in nonrigid molecules: the effect of fluctuating internuclear distances. J Chem Phys 72:6035-6043
    • (1980) J Chem Phys , vol.72 , pp. 6035-6043
    • Tropp, J.1
  • 80
    • 0000695363 scopus 로고    scopus 로고
    • High-resolution structure (1.33 angstrom) of a HEW lysozyme tetragonal crystal grown in the APCF apparatus. Data and structural comparison with a crystal grown under microgravity from SpaceHab-01 mission
    • Vaney MC, Maignan S, RiesKautt M, Ducruix A (1996) High-resolution structure (1.33 angstrom) of a HEW lysozyme tetragonal crystal grown in the APCF apparatus. Data and structural comparison with a crystal grown under microgravity from SpaceHab-01 mission. Acta Cryst D52:505-517
    • (1996) Acta Cryst , vol.D52 , pp. 505-517
    • Vaney, M.C.1    Maignan, S.2    RiesKautt, M.3    Ducruix, A.4
  • 81
    • 0037089015 scopus 로고    scopus 로고
    • Calculation of the free energy of solvation for neutral analogs of amino acid side chains
    • Villa A, Mark AE (2002) Calculation of the free energy of solvation for neutral analogs of amino acid side chains. J Comput Chem 23:548-553
    • (2002) J Comput Chem , vol.23 , pp. 548-553
    • Villa, A.1    Mark, A.E.2
  • 82
    • 0033719853 scopus 로고    scopus 로고
    • The effect of force-field parameters on properties of liquids: Parametrization of a simple three-site model for methanol
    • Walser R, Mark AE, Gunsteren WF van, Lauterbach M, Wipff G (2000) The effect of force-field parameters on properties of liquids: parametrization of a simple three-site model for methanol. J Chem Phys 112:10450-10459
    • (2000) J Chem Phys , vol.112 , pp. 10450-10459
    • Walser, R.1    Mark, A.E.2    Van Gunsteren, W.F.3    Lauterbach, M.4    Wipff, G.5
  • 83
    • 84986518863 scopus 로고
    • AMBER - Assisted model-building with energy refinement - A general program for modeling molecules and their interactions
    • Weiner PK, Kollman PA (1981) AMBER - assisted model-building with energy refinement - a general program for modeling molecules and their interactions. J Comput Chem 2:287-303
    • (1981) J Comput Chem , vol.2 , pp. 287-303
    • Weiner, P.K.1    Kollman, P.A.2
  • 84
    • 0021095743 scopus 로고
    • Pseudo-structures for the 20 common amino-acids for use in studies of protein conformations by measurements of intramolecular proton-proton distance constraints with nuclear magnetic resonance
    • Wüthrich K, Billeter M, Braun W (1983) Pseudo-structures for the 20 common amino-acids for use in studies of protein conformations by measurements of intramolecular proton-proton distance constraints with nuclear magnetic resonance. J Mol Biol 169:949-961
    • (1983) J Mol Biol , vol.169 , pp. 949-961
    • Wüthrich, K.1    Billeter, M.2    Braun, W.3
  • 85
    • 0031047279 scopus 로고    scopus 로고
    • Intrusion of counterions into the spine of hydration in the minor groove of B-DNA: Fractional occupancy of electronegative pockets
    • Young MA, Jayaram B, Beveridge DL (1997) Intrusion of counterions into the spine of hydration in the minor groove of B-DNA: fractional occupancy of electronegative pockets. J Am Chem Soc 119:59-69
    • (1997) J Am Chem Soc , vol.119 , pp. 59-69
    • Young, M.A.1    Jayaram, B.2    Beveridge, D.L.3


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