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Volumn 152, Issue 2, 2001, Pages 288-302

Internal coordinates for molecular dynamics and minimization in structure determination and refinement

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; G SUBSTRATE; G-SUBSTRATE; NERVE PROTEIN; PHOSPHOCARRIER PROTEIN HPR; PHOSPHOENOLPYRUVATE GLUCOSE PHOSPHOTRANSFERASE; PHOSPHOENOLPYRUVATE SUGAR PHOSPHOTRANSFERASE; PHOSPHOENOLPYRUVATE-GLUCOSE PHOSPHOTRANSFERASE;

EID: 0035742323     PISSN: 10907807     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmre.2001.2413     Document Type: Article
Times cited : (167)

References (39)
  • 1
    • 0000040038 scopus 로고
    • A fast recursive algorithm for molecular dynamics simulation
    • A. Jain N. Vaidehi G. Rodriguez A fast recursive algorithm for molecular dynamics simulation J. Comput. Phys. 106 1993 258
    • (1993) J. Comput. Phys. , vol.106 , pp. 258
    • Jain, A.1    Vaidehi, N.2    Rodriguez, G.3
  • 3
    • 84950199216 scopus 로고
    • A recursive formulation for constrained mechanical system dynamics: Part I. Open loop systems
    • Dae-Sung Bae E.J. Haug A recursive formulation for constrained mechanical system dynamics: Part I. Open loop systems Mech. Struct. Mach. 15 1987 359
    • (1987) Mech. Struct. Mach. , vol.15 , pp. 359
    • Bae, Dae-Sung1    Haug, E.J.2
  • 4
    • 84941502604 scopus 로고
    • A recursive formulation for constrained mechanical system dynamics: Part II. Closed loop systems
    • Dae-Sung Bae E.J. Haug A recursive formulation for constrained mechanical system dynamics: Part II. Closed loop systems Mech. Struct. Mach. 15 1987 481
    • (1987) Mech. Struct. Mach. , vol.15 , pp. 481
    • Bae, Dae-Sung1    Haug, E.J.2
  • 5
    • 0028070557 scopus 로고
    • Torsion angle dynamics: Reduced variable conformational sampling enhances crystallographic structure refinement
    • L.M. Rice A.T. Brünger Torsion angle dynamics: Reduced variable conformational sampling enhances crystallographic structure refinement Proteins 19 1994 277
    • (1994) Proteins , vol.19 , pp. 277
    • Rice, L.M.1    Brünger, A.T.2
  • 6
    • 0030621858 scopus 로고    scopus 로고
    • Torsion-angle molecular dynamics as a new efficient tool for NMR structure calculation
    • E.G. Stein L.M. Rice A.T. Brünger Torsion-angle molecular dynamics as a new efficient tool for NMR structure calculation J. Magn. Reson. 124 1997 154 164
    • (1997) J. Magn. Reson. , vol.124 , pp. 154-164
    • Stein, E.G.1    Rice, L.M.2    Brünger, A.T.3
  • 7
    • 0031576336 scopus 로고    scopus 로고
    • Torsion angle dynamics for NMR structure calculation with the new program Dyana
    • P. Güntert C. Mumenthaler K. Wüthrich Torsion angle dynamics for NMR structure calculation with the new program Dyana J. Mol. Biol. 273 1997 283
    • (1997) J. Mol. Biol. , vol.273 , pp. 283
    • Güntert, P.1    Mumenthaler, C.2    Wüthrich, K.3
  • 8
    • 0028063256 scopus 로고
    • Protein simulation using techniques suitable for very large systems: The cell multipole method for nonbond interactions and the Newton–Euler inverse mass operator method for internal coordinate dynamics
    • A.M. Mathiowetz A. Jain N. Karasawa W.A. Goddard III Protein simulation using techniques suitable for very large systems: The cell multipole method for nonbond interactions and the Newton–Euler inverse mass operator method for internal coordinate dynamics Proteins 20 1994 227
    • (1994) Proteins , vol.20 , pp. 227
    • Mathiowetz, A.M.1    Jain, A.2    Karasawa, N.3    Goddard, W.A.4
  • 9
    • 0003864349 scopus 로고    scopus 로고
    • Constant temperature constrained molecular dynamics: The Newton–Euler inverse mass operator method
    • N. Vaidehi A. Jain W.A. Goddard III Constant temperature constrained molecular dynamics: The Newton–Euler inverse mass operator method J. Phys. Chem. 100 1996 10,508
    • (1996) J. Phys. Chem. , vol.100
    • Vaidehi, N.1    Jain, A.2    Goddard, W.A.3
  • 10
    • 0032568556 scopus 로고    scopus 로고
    • New methods of structure refinement for macromolecular structure determination by NMR
    • G.M. Clore A.M. Gronenborn New methods of structure refinement for macromolecular structure determination by NMR Proc. Nat. Acad. Sci. U.S.A. 95 1998 5891 5898
    • (1998) Proc. Nat. Acad. Sci. U.S.A. , vol.95 , pp. 5891-5898
    • Clore, G.M.1    Gronenborn, A.M.2
  • 11
    • 85003411324 scopus 로고
    • Recursive flexible multibody system dynamics using spatial operators
    • A. Jain G. Rodriguez Recursive flexible multibody system dynamics using spatial operators J. Guid. Control Dynam. 15 1992 1453
    • (1992) J. Guid. Control Dynam. , vol.15 , pp. 1453
    • Jain, A.1    Rodriguez, G.2
  • 12
    • 85120221992 scopus 로고
    • H. Goldstein Classical Mechanics 1980 Addison–Wesley Reading
    • (1980)
    • Goldstein, H.1
  • 13
    • 0026205393 scopus 로고
    • A spatial operator algebra for manipulator modeling and control
    • G. Rodriguez A. Jain K. Kreutz-Delgado A spatial operator algebra for manipulator modeling and control Int. J. Rob. Res. 10 1991 371
    • (1991) Int. J. Rob. Res. , vol.10 , pp. 371
    • Rodriguez, G.1    Jain, A.2    Kreutz-Delgado, K.3
  • 14
    • 0000039979 scopus 로고    scopus 로고
    • Symplectic integration of closed chain rigid body dynamics with internal coordinate equations of motion
    • A.K. Mazur Symplectic integration of closed chain rigid body dynamics with internal coordinate equations of motion J. Chem. Phys. 111 1999 1407
    • (1999) J. Chem. Phys. , vol.111 , pp. 1407
    • Mazur, A.K.1
  • 15
    • 33646940952 scopus 로고
    • Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
    • J.P. Ryckaert G. Ciccotti H.J.C. Berendsen Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n -alkanes J. Comput. Phys. 23 1977 327
    • (1977) J. Comput. Phys. , vol.23 , pp. 327
    • Ryckaert, J.P.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 16
    • 84946450438 scopus 로고
    • Algorithms for macromolecular dynamics and constraint dynamics
    • W.F. van Gunsteren H.J.C. Berendsen Algorithms for macromolecular dynamics and constraint dynamics Mol. Phys. 34 1977 1311
    • (1977) Mol. Phys. , vol.34 , pp. 1311
    • van Gunsteren, W.F.1    Berendsen, H.J.C.2
  • 17
    • 1842692143 scopus 로고
    • A general definition of ring puckering coordinates
    • D. Cremer J.A. Pople A general definition of ring puckering coordinates J. Am. Chem. Soc. 76 1975 1354
    • (1975) J. Am. Chem. Soc. , vol.76 , pp. 1354
    • Cremer, D.1    Pople, J.A.2
  • 18
    • 22944467757 scopus 로고
    • Computer “experiments” on classical fluids. I. Thermodynamical Properties of Lennard–Jones molecules
    • L. Verlet Computer “experiments” on classical fluids. I. Thermodynamical Properties of Lennard–Jones molecules Phys. Rev. 159 1967 98
    • (1967) Phys. Rev. , vol.159 , pp. 98
    • Verlet, L.1
  • 20
    • 85120188670 scopus 로고
    • M.P. Allen D.J. Tildesley Computer Simulation of Liquid 1987 Clarendon Press Oxford p. 340
    • (1987)
    • Allen, M.P.1    Tildesley, D.J.2
  • 23
    • 34547809547 scopus 로고
    • A unified formulation of the constant temperature molecular dynamics methods
    • S. Nosé A unified formulation of the constant temperature molecular dynamics methods J. Chem. Phys. 81 1984 511
    • (1984) J. Chem. Phys. , vol.81 , pp. 511
    • Nosé, S.1
  • 24
    • 36449000062 scopus 로고
    • Nosé–Hoover chains: The canonical ensemble via continuous dynamics
    • G.J. Martyna M.L. Klein M. Tuckerman Nosé–Hoover chains: The canonical ensemble via continuous dynamics J. Chem. Phys. 97 1992 2635
    • (1992) J. Chem. Phys. , vol.97 , pp. 2635
    • Martyna, G.J.1    Klein, M.L.2    Tuckerman, M.3
  • 25
    • 33846446220 scopus 로고
    • Restart procedures for the conjugate gradient method
    • M.J.D. Powell Restart procedures for the conjugate gradient method Math. Program. 12 1977 241 254
    • (1977) Math. Program. , vol.12 , pp. 241-254
    • Powell, M.J.D.1
  • 26
    • 84947409756 scopus 로고
    • Singularity free algorithm for molecular dynamics simulation of rigid polyatomics
    • D.J. Evans S. Murad Singularity free algorithm for molecular dynamics simulation of rigid polyatomics Mol. Phys. 34 1977 327
    • (1977) Mol. Phys. , vol.34 , pp. 327
    • Evans, D.J.1    Murad, S.2
  • 27
    • 85120226721 scopus 로고
    • H. Goldstein Classical Mechanics 1980 Addison–Wesley Reading p. 608
    • (1980)
    • Goldstein, H.1
  • 28
    • 0031414754 scopus 로고    scopus 로고
    • Structural studies of the Escherichia coli signal transducing protein IIA(Glc): Implications for target recognition
    • M.D. Feese L. Comolli N.D. Meadow S. Roseman S.J. Remington Structural studies of the Escherichia coli signal transducing protein IIA(Glc): Implications for target recognition Biochem. 36 1997 16,087
    • (1997) Biochem. , vol.36
    • Feese, M.D.1    Comolli, L.2    Meadow, N.D.3    Roseman, S.4    Remington, S.J.5
  • 29
    • 0027340388 scopus 로고
    • The 2.0-angstrom resolution structure of escherichia-coli histidine-containing phosphocarrier protein HPr—A redetermination
    • Z.C. Jia J.W. Quail E.B. Waygood L.T.J. Delbaere The 2.0-angstrom resolution structure of escherichia-coli histidine-containing phosphocarrier protein HPr—A redetermination J. Biol. Chem. 268 1993 22,490
    • (1993) J. Biol. Chem. , vol.268
    • Jia, Z.C.1    Quail, J.W.2    Waygood, E.B.3    Delbaere, L.T.J.4
  • 30
    • 0034329415 scopus 로고    scopus 로고
    • Solution structure of the phosphoryl transfer complex between the signal transducing proteins HPr and IIA(Glucose) of the Escherichia coli phosphoenolpyruvate: Sugar phosphotransferase system
    • G.S. Wang J.M. Louis M. Sondej Y.J. Seok A. Peterkofsky G.M. Clore Solution structure of the phosphoryl transfer complex between the signal transducing proteins HPr and IIA(Glucose) of the Escherichia coli phosphoenolpyruvate: Sugar phosphotransferase system EMBO J. 19 2000 5635
    • (2000) EMBO J. , vol.19 , pp. 5635
    • Wang, G.S.1    Louis, J.M.2    Sondej, M.3    Seok, Y.J.4    Peterkofsky, A.5    Clore, G.M.6
  • 31
    • 0034254909 scopus 로고    scopus 로고
    • Accurate and rapid docking of protein–protein complexes on the basis of intermolecular nuclear Overhauser enhancement data and dipolar couplings by rigid body minimization
    • G.M. Clore Accurate and rapid docking of protein–protein complexes on the basis of intermolecular nuclear Overhauser enhancement data and dipolar couplings by rigid body minimization P. Nat. Acad. Sci. USA 97 2000 9021
    • (2000) P. Nat. Acad. Sci. USA , vol.97 , pp. 9021
    • Clore, G.M.1
  • 32
    • 0033577269 scopus 로고    scopus 로고
    • Improving the packing and accuracy of NMR structures with a pseudopotential for the radius of gyration
    • J. Kuszewski A.M. Gronenborn G.M. Clore Improving the packing and accuracy of NMR structures with a pseudopotential for the radius of gyration J. Am. Chem. Soc. 121 1999 2337
    • (1999) J. Am. Chem. Soc. , vol.121 , pp. 2337
    • Kuszewski, J.1    Gronenborn, A.M.2    Clore, G.M.3
  • 33
    • 0034296491 scopus 로고    scopus 로고
    • Source of and solutions to problems in the refinement of protein NMR structures against torsion angle potentials of mean force
    • J. Kuszewski G.M. Clore Source of and solutions to problems in the refinement of protein NMR structures against torsion angle potentials of mean force J. Magn. Reson. 146 2000 249 254
    • (2000) J. Magn. Reson. , vol.146 , pp. 249-254
    • Kuszewski, J.1    Clore, G.M.2
  • 34
    • 0032012610 scopus 로고    scopus 로고
    • Direct refinement against residual dipolar couplings in the presence of rhombicity of unknown magnitude
    • G.M. Clore A.M. Gronenborn N. Tjandra Direct refinement against residual dipolar couplings in the presence of rhombicity of unknown magnitude J. Magn. Reson. 131 1998 159 162
    • (1998) J. Magn. Reson. , vol.131 , pp. 159-162
    • Clore, G.M.1    Gronenborn, A.M.2    Tjandra, N.3
  • 35
    • 0035742163 scopus 로고    scopus 로고
    • The VMD–XPLOR visualization package for NMR structure refinement
    • C.D. Schwieters G.M. Clore The VMD–XPLOR visualization package for NMR structure refinement J. Magn. Reson. 149 2001 239
    • (2001) J. Magn. Reson. , vol.149 , pp. 239
    • Schwieters, C.D.1    Clore, G.M.2
  • 37
    • 0000525633 scopus 로고
    • Effect of constraints on the dynamics of macromolecules
    • W.F. van Gunsteren M. Karplus Effect of constraints on the dynamics of macromolecules Macromolecules 15 1982 1528
    • (1982) Macromolecules , vol.15 , pp. 1528
    • van Gunsteren, W.F.1    Karplus, M.2
  • 38
    • 84986483801 scopus 로고
    • A truncated Newton minimizer adapted for CHARMM and biomolecular applications
    • P. Derreumaux G. Zhang T. Schlick B. Brooks A truncated Newton minimizer adapted for CHARMM and biomolecular applications J. Comput. Chem. 15 1994 532
    • (1994) J. Comput. Chem. , vol.15 , pp. 532
    • Derreumaux, P.1    Zhang, G.2    Schlick, T.3    Brooks, B.4
  • 39
    • 0033269652 scopus 로고    scopus 로고
    • Efficient implementation of the truncated-Newton algorithm for large-scale chemistry applications
    • D.X. Xie T. Schlick Efficient implementation of the truncated-Newton algorithm for large-scale chemistry applications SIAM J. Optimiz. 10 1999 132
    • (1999) SIAM J. Optimiz. , vol.10 , pp. 132
    • Xie, D.X.1    Schlick, T.2


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