-
1
-
-
0026320866
-
The energy landscapes and motions of proteins
-
Frauenfelder, H., Sligar, S.G., Wolynes, P.G. The energy landscapes and motions of proteins. Science 254:1598-1603, 1991.
-
(1991)
Science
, vol.254
, pp. 1598-1603
-
-
Frauenfelder, H.1
Sligar, S.G.2
Wolynes, P.G.3
-
2
-
-
0002237761
-
Biomolecules: Where the Physics of complexity and simplicity meet
-
Frauenfelder, H., Wolynes, P.G. Biomolecules: Where the Physics of complexity and simplicity meet. Physics Today February 47:58-64, 1994.
-
(1994)
Physics Today February
, vol.47
, pp. 58-64
-
-
Frauenfelder, H.1
Wolynes, P.G.2
-
3
-
-
0029099219
-
Looking into the energy landscape of myoglobin: Evidence for self-similarity
-
Leeson, D.T., Wiersma, D.A. Looking into the energy landscape of myoglobin: Evidence for self-similarity. Nat. Struct. Biol. 2:848-851, 1995.
-
(1995)
Nat. Struct. Biol.
, vol.2
, pp. 848-851
-
-
Leeson, D.T.1
Wiersma, D.A.2
-
4
-
-
0023140044
-
Multiple conformational states of proteins: A molecular dynamics analysis of myoglobin
-
Elber, R., Karplus, M. Multiple conformational states of proteins: A molecular dynamics analysis of myoglobin. Science 235:318-321, 1987.
-
(1987)
Science
, vol.235
, pp. 318-321
-
-
Elber, R.1
Karplus, M.2
-
5
-
-
0024585391
-
Structural basis of hierarchical multiple substates of a protein. I: Introduction
-
Noguti, T., Go, N. Structural basis of hierarchical multiple substates of a protein. I: Introduction. Proteins 5:97-103, 1989.
-
(1989)
Proteins
, vol.5
, pp. 97-103
-
-
Noguti, T.1
Go, N.2
-
6
-
-
0024567779
-
Structural basis of hierarchical multiple substates of a protein. II: Monte Carlo simulation of native thermal fluctuations and energy minimization
-
Noguti, T., Go, N. Structural basis of hierarchical multiple substates of a protein. II: Monte Carlo simulation of native thermal fluctuations and energy minimization. Proteins 5:104-112, 1989.
-
(1989)
Proteins
, vol.5
, pp. 104-112
-
-
Noguti, T.1
Go, N.2
-
7
-
-
0024486487
-
Structural basis of hierarchical multiple substates of a protein. III: Side chain and main chain local conformations
-
Noguti, T., Go, N. Structural basis of hierarchical multiple substates of a protein. III: Side chain and main chain local conformations. Proteins 5:113-124, 1989.
-
(1989)
Proteins
, vol.5
, pp. 113-124
-
-
Noguti, T.1
Go, N.2
-
8
-
-
0024486623
-
Structural basis of hierarchical multiple substates of a protein. IV: Rearrangements in atom packing and local deformations
-
Noguti, T., Go, N. Structural basis of hierarchical multiple substates of a protein. IV: Rearrangements in atom packing and local deformations. Proteins 5:125-131, 1989.
-
(1989)
Proteins
, vol.5
, pp. 125-131
-
-
Noguti, T.1
Go, N.2
-
9
-
-
0024486201
-
Structural basis of hierarchical multiple substates of a protein. V: Nonlocal deformations
-
Noguti, T., Go, N. Structural basis of hierarchical multiple substates of a protein. V: Nonlocal deformations. Proteins 5:132-138, 1989.
-
(1989)
Proteins
, vol.5
, pp. 132-138
-
-
Noguti, T.1
Go, N.2
-
10
-
-
0029152775
-
Protein conformational landscapes: Energy minimization and clustering of a long molecular dynamics trajectory
-
Troyer, J.M., Cohen, F.E. Protein conformational landscapes: Energy minimization and clustering of a long molecular dynamics trajectory. Proteins 23:97-110, 1995.
-
(1995)
Proteins
, vol.23
, pp. 97-110
-
-
Troyer, J.M.1
Cohen, F.E.2
-
11
-
-
0021449809
-
Quasi-harmonic method for studying very low frequency modes in proteins
-
Levy, R.M., Srinivasan, A.R., Olson, W.K., McCammon, JA. Quasi-harmonic method for studying very low frequency modes in proteins. Biopolymers 23:1099-1112, 1984.
-
(1984)
Biopolymers
, vol.23
, pp. 1099-1112
-
-
Levy, R.M.1
Srinivasan, A.R.2
Olson, W.K.3
McCammon, J.A.4
-
12
-
-
0000998079
-
The effects of solvent on the conformation and the collective motions of protein: Normal mode analysis and molecular dynamics simulation of melittin in water and in vacuum
-
Kitao, A., Hirata, F., Go, N. The effects of solvent on the conformation and the collective motions of protein: Normal mode analysis and molecular dynamics simulation of melittin in water and in vacuum. Chem. Phys. 158:447-472, 1991.
-
(1991)
Chem. Phys.
, vol.158
, pp. 447-472
-
-
Kitao, A.1
Hirata, F.2
Go, N.3
-
13
-
-
0000577041
-
Large-amplitude nonlinear motions in proteins
-
García, A.E. Large-amplitude nonlinear motions in proteins. Phys. Rev. Lett. 68:2696-2699, 1992.
-
(1992)
Phys. Rev. Lett.
, vol.68
, pp. 2696-2699
-
-
García, A.E.1
-
14
-
-
0027732618
-
Effect of solvent on collective motions in globular proteins
-
Hayward, S., Kitao, A., Hirata, F., Go, N. Effect of solvent on collective motions in globular proteins. J. Mol. Biol. 234:1207-1217, 1993.
-
(1993)
J. Mol. Biol.
, vol.234
, pp. 1207-1217
-
-
Hayward, S.1
Kitao, A.2
Hirata, F.3
Go, N.4
-
15
-
-
0028292635
-
Harmonic and anharmonic effects in the dynamics of BPTI: A normal mode analysis and principal component analysis
-
Hayward, S., Kitao, A., Go, N. Harmonic and anharmonic effects in the dynamics of BPTI: A normal mode analysis and principal component analysis. Protein Sci. 3:936-943, 1994.
-
(1994)
Protein Sci.
, vol.3
, pp. 936-943
-
-
Hayward, S.1
Kitao, A.2
Go, N.3
-
16
-
-
0028877423
-
Harmonicity and anharmonicity in protein dynamics: A normal mode analysis and principal component analysis
-
Hayward, S., Kitao, A., Go, N. Harmonicity and anharmonicity in protein dynamics: a normal mode analysis and principal component analysis. Proteins 23:177-186, 1995
-
(1995)
Proteins
, vol.23
, pp. 177-186
-
-
Hayward, S.1
Kitao, A.2
Go, N.3
-
17
-
-
0027441950
-
Essential dynamics of proteins
-
Amadei, A., Linssen, A.B.M., Berendsen, H.J.C. Essential dynamics of proteins. Proteins 17:412-425, 1993.
-
(1993)
Proteins
, vol.17
, pp. 412-425
-
-
Amadei, A.1
Linssen, A.B.M.2
Berendsen, H.J.C.3
-
18
-
-
0026717834
-
Normal mode refinement: Crystallographic refinement of protein dynamic structure. II. Application to human lysozyme
-
Kidera, A., Inaka, K., Matsushima, M., Go, N. Normal mode refinement: Crystallographic refinement of protein dynamic structure. II. Application to human lysozyme. J. Mol. Biol. 225:477-486, 1992.
-
(1992)
J. Mol. Biol.
, vol.225
, pp. 477-486
-
-
Kidera, A.1
Inaka, K.2
Matsushima, M.3
Go, N.4
-
19
-
-
0029150760
-
Protein flexibility and adaptability seen in 25 crystal forms of T4 lysozyme
-
Zhang, X., Woxniak, J.A., Matthews, B.W. Protein flexibility and adaptability seen in 25 crystal forms of T4 lysozyme. J. Mol. Biol. 250:527-552, 1995.
-
(1995)
J. Mol. Biol.
, vol.250
, pp. 527-552
-
-
Zhang, X.1
Woxniak, J.A.2
Matthews, B.W.3
-
20
-
-
0017163950
-
Hinge bending mode in lysozyme
-
McCammon, J.A., Gelin, B.R., Karplus, M., Wolynes, P.G. Hinge bending mode in lysozyme. Nature 262:325-326, 1976.
-
(1976)
Nature
, vol.262
, pp. 325-326
-
-
McCammon, J.A.1
Gelin, B.R.2
Karplus, M.3
Wolynes, P.G.4
-
21
-
-
0022111715
-
Normal modes for specific motions of macromolecules: Application to the hinge bending mode of lysozyme
-
Brooks, B., Karplus, M. Normal modes for specific motions of macromolecules: Application to the hinge bending mode of lysozyme. Proc. Natl. Acad. Sci. USA 82:4995-4999, 1985.
-
(1985)
Proc. Natl. Acad. Sci. USA
, vol.82
, pp. 4995-4999
-
-
Brooks, B.1
Karplus, M.2
-
22
-
-
0023042577
-
Molecular dynamics simulations of native and substrate-bound lysozyme
-
Post, C.B., Brooks, B.R., Karplus, M., Dobson, C.M., Artymiuk, P.J., Cheetham, J.C., Phillips, D.C. Molecular dynamics simulations of native and substrate-bound lysozyme. J. Mol. Biol. 190:455-479, 1986.
-
(1986)
J. Mol. Biol.
, vol.190
, pp. 455-479
-
-
Post, C.B.1
Brooks, B.R.2
Karplus, M.3
Dobson, C.M.4
Artymiuk, P.J.5
Cheetham, J.C.6
Phillips, D.C.7
-
23
-
-
0023512803
-
Anisotropy and anharmonicity of the atomic fluctuations in proteins: Analysis of a molecular dynamics simulation
-
Ichiye, T., Karplus, M. Anisotropy and anharmonicity of the atomic fluctuations in proteins: Analysis of a molecular dynamics simulation. Proteins 2:236-259, 1987.
-
(1987)
Proteins
, vol.2
, pp. 236-259
-
-
Ichiye, T.1
Karplus, M.2
-
24
-
-
0024354001
-
Solvent effects on protein motion and protein effects on solvent motion
-
Brooks III, C.L., Karplus, M. Solvent effects on protein motion and protein effects on solvent motion. J. Mol. Biol. 208:159-181, 1989.
-
(1989)
J. Mol. Biol.
, vol.208
, pp. 159-181
-
-
Brooks III, C.L.1
Karplus, M.2
-
25
-
-
0029162947
-
Comparison of MD simulations and NMR experiments for hen lysozyme. Analysis of local fluctuations, cooperative motions, and global changes
-
Smith, L.J., Mark, A.E., Dobson, C.M., van Gunsteren, W.F. Comparison of MD simulations and NMR experiments for hen lysozyme. Analysis of local fluctuations, cooperative motions, and global changes. Biochemistry 34:10918-10931, 1995.
-
(1995)
Biochemistry
, vol.34
, pp. 10918-10931
-
-
Smith, L.J.1
Mark, A.E.2
Dobson, C.M.3
Van Gunsteren, W.F.4
-
26
-
-
0025066772
-
Normal mode analysis of human lysozyme: Study of the relative motion of the two domains and characterization of the harmonic motion
-
Gibrat, J., Go, N. Normal mode analysis of human lysozyme: Study of the relative motion of the two domains and characterization of the harmonic motion. Proteins 8:258-279, 1990.
-
(1990)
Proteins
, vol.8
, pp. 258-279
-
-
Gibrat, J.1
Go, N.2
-
27
-
-
0025753631
-
Projection of Monte Carlo and molecular dynamics trajectories onto the normal mode axes: Human lysozyme
-
Horiuchi, T., Go, N. Projection of Monte Carlo and molecular dynamics trajectories onto the normal mode axes: Human lysozyme. Proteins 10:106-116, 1991.
-
(1991)
Proteins
, vol.10
, pp. 106-116
-
-
Horiuchi, T.1
Go, N.2
-
28
-
-
0026459304
-
A molecular dynamics simulation of bacteriophage T4 lysozyme
-
Arnold, G.E., Ornstein, R.L. A molecular dynamics simulation of bacteriophage T4 lysozyme. Protein Eng. 5:703-714, 1992.
-
(1992)
Protein Eng.
, vol.5
, pp. 703-714
-
-
Arnold, G.E.1
Ornstein, R.L.2
-
29
-
-
0030888546
-
Model-free methods of analyzing domain motions in proteins from simulations: A comparison of normal mode analysis and molecular dynamics simulation of lysozyme
-
Hayward, S., Kitao, A., Berendsen, H.J.C. Model-free methods of analyzing domain motions in proteins from simulations: A comparison of normal mode analysis and molecular dynamics simulation of lysozyme. Proteins 27: 425-437, 1997.
-
(1997)
Proteins
, vol.27
, pp. 425-437
-
-
Hayward, S.1
Kitao, A.2
Berendsen, H.J.C.3
-
30
-
-
0032032108
-
Improved Protein Free Energy Calculation by More Accurate Treatment of Nonbonded Energy: Application to Chymotrypsin Inhibitor 2, V57A
-
Sugita, Y., Kitao, A. Improved Protein Free Energy Calculation by More Accurate Treatment of Nonbonded Energy: Application to Chymotrypsin Inhibitor 2, V57A. Proteins 30:388-400, 1998.
-
(1998)
Proteins
, vol.30
, pp. 388-400
-
-
Sugita, Y.1
Kitao, A.2
-
31
-
-
0001655657
-
Finite representation of an infinite bulk system: Solvent boundary potential for computer simulations
-
Beglov, D., Roux, B. Finite representation of an infinite bulk system: Solvent boundary potential for computer simulations. J. Chem. Phys. 100:9050-9063, 1994.
-
(1994)
J. Chem. Phys.
, vol.100
, pp. 9050-9063
-
-
Beglov, D.1
Roux, B.2
-
32
-
-
5244247401
-
Atomic level simulations on million particles: The cell multipole method for Coulomb and London nonbond interactions
-
Ding, H.-Q., Karasawa, N., Goddard III, W.A. Atomic level simulations on million particles: The cell multipole method for Coulomb and London nonbond interactions. J. Chem. Phys. 97:4309-4315, 1992.
-
(1992)
J. Chem. Phys.
, vol.97
, pp. 4309-4315
-
-
Ding, H.-Q.1
Karasawa, N.2
Goddard III, W.A.3
-
33
-
-
84943502952
-
A molecular dynamics method for simulations in the canonical ensemble
-
Nosé, S. A molecular dynamics method for simulations in the canonical ensemble. Mol. Phys. 52:255-268, 1984.
-
(1984)
Mol. Phys.
, vol.52
, pp. 255-268
-
-
Nosé, S.1
-
34
-
-
0001538909
-
Canonical dynamics: Equilibrium phase-space distributions
-
Hoover, W.G. Canonical dynamics: Equilibrium phase-space distributions. Phys. Rev. A31:1695-1697, 1985.
-
(1985)
Phys. Rev.
, vol.A31
, pp. 1695-1697
-
-
Hoover, W.G.1
-
35
-
-
84988053694
-
An all atom force field for simulations of proteins and nucleic acids
-
Weiner, S.J., Kollman, P.A., Nguyen, D.T., Case, D.A. An all atom force field for simulations of proteins and nucleic acids J. Comp. Chem. 7:230-252, 1986.
-
(1986)
J. Comp. Chem.
, vol.7
, pp. 230-252
-
-
Weiner, S.J.1
Kollman, P.A.2
Nguyen, D.T.3
Case, D.A.4
-
36
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
Jorgensen, W.L., Chandrasekhar, J., Madura, J.D. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79:926-935, 1983.
-
(1983)
J. Chem. Phys.
, vol.79
, pp. 926-935
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Madura, J.D.3
-
38
-
-
84986472098
-
Conformational dynamics of polypeptides and proteins in the dihedral angle space and in the cartesian coordinate space: Normal mode analysis of decaalanine
-
Kitao, A., Go, N. Conformational dynamics of polypeptides and proteins in the dihedral angle space and in the cartesian coordinate space: Normal mode analysis of decaalanine. J. Comp. Chem. 12:359-368, 1991.
-
(1991)
J. Comp. Chem.
, vol.12
, pp. 359-368
-
-
Kitao, A.1
Go, N.2
-
39
-
-
36149010019
-
Some Studies Concerning Rotating Axes and Polyatomic Molecules
-
Eckart, C. Some Studies Concerning Rotating Axes and Polyatomic Molecules. Phys. Rev. 47:552-558, 1935.
-
(1935)
Phys. Rev.
, vol.47
, pp. 552-558
-
-
Eckart, C.1
-
40
-
-
0027983643
-
Comparison of normal mode analyses on a small globular protein in dihedral angle space and cartesian coordinate space
-
Kitao, A., Hayward, S., Go, N. Comparison of normal mode analyses on a small globular protein in dihedral angle space and cartesian coordinate space. Biophys. Chem. 52:107-114, 1994.
-
(1994)
Biophys. Chem.
, vol.52
, pp. 107-114
-
-
Kitao, A.1
Hayward, S.2
Go, N.3
-
41
-
-
3743054071
-
Normal mode analysis of a nucleic acid with flexible furanose rings in dihedral angle space
-
Tomimoto, M., Kitao, A., Go, N. Normal mode analysis of a nucleic acid with flexible furanose rings in dihedral angle space. Electro. J. Theor. Chem. 1:122-134, 1996.
-
(1996)
Electro. J. Theor. Chem.
, vol.1
, pp. 122-134
-
-
Tomimoto, M.1
Kitao, A.2
Go, N.3
-
42
-
-
0028786432
-
Contribution of hydrophobic residues to the stability of human lysozyme: Calorimetric studies and X-ray structural analysis of the five isoleucine to valine mutants
-
Takano, K., Ogasahara, K., Kaneda, H. et al. Contribution of hydrophobic residues to the stability of human lysozyme: Calorimetric studies and X-ray structural analysis of the five isoleucine to valine mutants. J. Mol. Biol. 254:62-76, 1995.
-
(1995)
J. Mol. Biol.
, vol.254
, pp. 62-76
-
-
Takano, K.1
Ogasahara, K.2
Kaneda, H.3
-
43
-
-
0019816864
-
Refinement of human lysozyme at 1.5Å resolution analysis of non-bonded and hydrogen-bonded interactions
-
Artymuik, P.J., Blake, C.C.F. Refinement of human lysozyme at 1.5Å resolution analysis of non-bonded and hydrogen-bonded interactions. J. Mol. Biol. 152:737-762, 1981.
-
(1981)
J. Mol. Biol.
, vol.152
, pp. 737-762
-
-
Artymuik, P.J.1
Blake, C.C.F.2
-
44
-
-
36149005118
-
On the theory of the Brownian motion
-
Uhlenbeck, G.E., Ornstein, L.S. On the theory of the Brownian motion. Phys. Rev. 36:823-841, 1930.
-
(1930)
Phys. Rev.
, vol.36
, pp. 823-841
-
-
Uhlenbeck, G.E.1
Ornstein, L.S.2
-
45
-
-
0002121327
-
Stochastic problems in physics and astronomy
-
Chandrasekhar, S. Stochastic problems in physics and astronomy. Reviews of Modern Physics 15:1-89, 1943.
-
(1943)
Reviews of Modern Physics
, vol.15
, pp. 1-89
-
-
Chandrasekhar, S.1
-
46
-
-
0020771265
-
Dynamics of a small globular protein in terms of low-frequency vibrational modes
-
Go, N., Noguti, T., Nishikawa, T. Dynamics of a small globular protein in terms of low-frequency vibrational modes. Proc. Natl. Acad. Sci. USA 80:3696-3700, 1983.
-
(1983)
Proc. Natl. Acad. Sci. USA
, vol.80
, pp. 3696-3700
-
-
Go, N.1
Noguti, T.2
Nishikawa, T.3
-
47
-
-
0023613529
-
Normal modes of vibration in bovine pancreatic inhibitor and its mechanical properties
-
Nishikawa, T., Go, N. Normal modes of vibration in bovine pancreatic inhibitor and its mechanical properties. Proteins 2:308-329, 1987.
-
(1987)
Proteins
, vol.2
, pp. 308-329
-
-
Nishikawa, T.1
Go, N.2
-
48
-
-
0026663419
-
Normal mode refinement: Crystallographic refinement of protein dynamic structure. I. Theory and test by simulated diffraction data
-
Kidera, A., Go, N. Normal mode refinement: Crystallographic refinement of protein dynamic structure. I. Theory and test by simulated diffraction data. J. Mol. Biol. 225:457-475, 1992.
-
(1992)
J. Mol. Biol.
, vol.225
, pp. 457-475
-
-
Kidera, A.1
Go, N.2
-
49
-
-
0000081668
-
Collective variable description of native protein dynamics
-
Hayward, S., Go, N. Collective variable description of native protein dynamics. Annu. Rev. Phys. Chem. 46:223-250, 1995.
-
(1995)
Annu. Rev. Phys. Chem.
, vol.46
, pp. 223-250
-
-
Hayward, S.1
Go, N.2
-
50
-
-
0025938315
-
Protein dynamics: Comparison of simulations with inelastic neutron scattering experiments
-
Smith, J.C. Protein dynamics: comparison of simulations with inelastic neutron scattering experiments. Q. Rev. Biophys. 24:227-291, 1991.
-
(1991)
Q. Rev. Biophys.
, vol.24
, pp. 227-291
-
-
Smith, J.C.1
-
51
-
-
0000078368
-
Effects of solvent on the conformation and the collective motions of a protein. 2. Structure of hydration in melittin
-
Kitao, A., Hirata, F., Go, N. Effects of solvent on the conformation and the collective motions of a protein. 2. Structure of hydration in melittin. J. Phys. Chem. 97: 10223-10230, 1993.
-
(1993)
J. Phys. Chem.
, vol.97
, pp. 10223-10230
-
-
Kitao, A.1
Hirata, F.2
Go, N.3
-
52
-
-
0000078369
-
Effects of solvent on the conformation and the collective motions of a protein. 3. Free energy analysis by the extended RISM Theory
-
Kitao, A., Hirata, F., Go, N. Effects of solvent on the conformation and the collective motions of a protein. 3. Free energy analysis by the extended RISM Theory. J. Phys. Chem. 97:10231-10235, 1993.
-
(1993)
J. Phys. Chem.
, vol.97
, pp. 10231-10235
-
-
Kitao, A.1
Hirata, F.2
Go, N.3
-
53
-
-
0000902576
-
Structural basis of hierarchical multiple substates of a protein
-
Go, N., Noguti, T. Structural basis of hierarchical multiple substates of a protein. Chemica Scripta 29A:151-164, 1989.
-
(1989)
Chemica Scripta
, vol.29 A
, pp. 151-164
-
-
Go, N.1
Noguti, T.2
-
54
-
-
0000999856
-
Structural relaxations in H2-substituted myoglobin observed by temperature-cycling hole burning
-
Shibata, Y., Kurita, A., Kushida, T. Structural relaxations in H2-substituted myoglobin observed by temperature-cycling hole burning. J. Chem. Phys. 104:4396-4405, 1996.
-
(1996)
J. Chem. Phys.
, vol.104
, pp. 4396-4405
-
-
Shibata, Y.1
Kurita, A.2
Kushida, T.3
-
55
-
-
0026890721
-
Structural dynamics of proteins investigated by hole-burning spectroscopy
-
Kurita, A., Ohmukai, R., Kushida, T. Structural dynamics of proteins investigated by hole-burning spectroscopy. Journal of Luminescence 53:255-258, 1992.
-
(1992)
Journal of Luminescence
, vol.53
, pp. 255-258
-
-
Kurita, A.1
Ohmukai, R.2
Kushida, T.3
-
56
-
-
0010425813
-
Two-level systems in myoglobin probed by non-lorenzian hole broadening in temperature-cycling experiment
-
Kurita, A., Shibata, Y., Kushida, T. Two-level systems in myoglobin probed by non-lorenzian hole broadening in temperature-cycling experiment. Phys. Rev. Lett. 74:4349-4352, 1995.
-
(1995)
Phys. Rev. Lett.
, vol.74
, pp. 4349-4352
-
-
Kurita, A.1
Shibata, Y.2
Kushida, T.3
-
58
-
-
0008994613
-
Extracting the energy barrier distribution of a disordered system from the instantaneous normal mode density of states: Applications to peptides and proteins
-
Straub, J.E., Choi, J.-K. Extracting the energy barrier distribution of a disordered system from the instantaneous normal mode density of states: Applications to peptides and proteins. J. Phys. Chem. 98:10978-10987, 1994.
-
(1994)
J. Phys. Chem.
, vol.98
, pp. 10978-10987
-
-
Straub, J.E.1
Choi, J.-K.2
-
59
-
-
0000885331
-
Harmonic analysis of large systems. I. Methodology
-
Brooks, B.R., Janezic, D., Karplus, M. Harmonic analysis of large systems. I. Methodology. J. Comp. Chem. 16:1522-1542, 1995.
-
(1995)
J. Comp. Chem.
, vol.16
, pp. 1522-1542
-
-
Brooks, B.R.1
Janezic, D.2
Karplus, M.3
-
60
-
-
84986469420
-
Harmonic analysis of large systems. II. Comparison of different protein models
-
Janezic, D., Brooks, B.R. Harmonic analysis of large systems. II. Comparison of different protein models. J. Comp. Chem. 16:1543-1553, 1995.
-
(1995)
J. Comp. Chem.
, vol.16
, pp. 1543-1553
-
-
Janezic, D.1
Brooks, B.R.2
-
61
-
-
84986473952
-
Harmonic analysis of large systems. III. Comparison with molecular dynamics
-
Janezic, D., Veneble, R.M., Brooks, B.R. Harmonic analysis of large systems. III. Comparison with molecular dynamics. J. Comp. Chem. 16:1554-1566, 1995.
-
(1995)
J. Comp. Chem.
, vol.16
, pp. 1554-1566
-
-
Janezic, D.1
Veneble, R.M.2
Brooks, B.R.3
-
62
-
-
0029022540
-
Anharmonic wave functions of proteins: Quantum self-consistent field calculations of BPTI
-
Roitberg, A., Gerber, R.B., Elber, R., Ratner, M.A. Anharmonic wave functions of proteins: Quantum self-consistent field calculations of BPTI. Science 268:1319-1322, 1995.
-
(1995)
Science
, vol.268
, pp. 1319-1322
-
-
Roitberg, A.1
Gerber, R.B.2
Elber, R.3
Ratner, M.A.4
-
63
-
-
0027975255
-
10-/α-helix transition: Implications for a natural reaction coordinate
-
10-/α-helix transition: Implications for a natural reaction coordinate. J. Am. Chem. Soc. 116:6307-6315, 1994.
-
(1994)
J. Am. Chem. Soc.
, vol.116
, pp. 6307-6315
-
-
Basu, G.1
Kitao, A.2
Hirata, F.3
Go, N.4
-
64
-
-
0027254295
-
Conformational classification of short backbone fragments in globular proteins and its use for coding backbone conformations
-
Takahashi, K., Go, N. Conformational classification of short backbone fragments in globular proteins and its use for coding backbone conformations. Biophys. Chem. 47:163-178, 1993.
-
(1993)
Biophys. Chem.
, vol.47
, pp. 163-178
-
-
Takahashi, K.1
Go, N.2
-
65
-
-
0000980795
-
Quasi-harmonic method for calculating vibrational spectra from classica simulations on multidimensional anharmonic potential surfaces
-
Levy, R.M., Rojas, O.L., Friesner, R.A. Quasi-harmonic method for calculating vibrational spectra from classica simulations on multidimensional anharmonic potential surfaces. J. Phys. Chem. 88:4233-4238, 1984.
-
(1984)
J. Phys. Chem.
, vol.88
, pp. 4233-4238
-
-
Levy, R.M.1
Rojas, O.L.2
Friesner, R.A.3
-
66
-
-
0024094768
-
Accurate simulation of protein dynamics in solution
-
Levitt, M., Sharon, R. Accurate simulation of protein dynamics in solution. Proc. Natl. Acad. Sci. USA 85:7557-7561, 1988.
-
(1988)
Proc. Natl. Acad. Sci. USA
, vol.85
, pp. 7557-7561
-
-
Levitt, M.1
Sharon, R.2
-
67
-
-
0024795316
-
The effects of truncating long-range forces on protein dynamics
-
Loncharich, R.J., Brooks, B.R. The effects of truncating long-range forces on protein dynamics. Proteins 6:32-45, 1989.
-
(1989)
Proteins
, vol.6
, pp. 32-45
-
-
Loncharich, R.J.1
Brooks, B.R.2
-
68
-
-
36449006641
-
Molecular dynamics simulations of proteins in solution: Artifacts caused by the cutoff approximation
-
Saito, M. Molecular dynamics simulations of proteins in solution: Artifacts caused by the cutoff approximation. J. Chem. Phys. 101:4055-4061, 1994.
-
(1994)
J. Chem. Phys.
, vol.101
, pp. 4055-4061
-
-
Saito, M.1
-
69
-
-
0028068802
-
Atomic-level accuracy in simulations of large protein crystals
-
York, D.M., Wlodawer, A., Pedersen, L.G., Darden, T.A. Atomic-level accuracy in simulations of large protein crystals Proc. Natl. Acad. Sci. USA 91:8715-8718, 1994.
-
(1994)
Proc. Natl. Acad. Sci. USA
, vol.91
, pp. 8715-8718
-
-
York, D.M.1
Wlodawer, A.2
Pedersen, L.G.3
Darden, T.A.4
-
70
-
-
0008348735
-
PRESTO (Protein Engineering SimulaTOr): A vectorized molecular mechamics program for biopolymers
-
Morikami, K., Nakai, T., Kidera, M., Saito, M., Nakamura, H. PRESTO (Protein Engineering SimulaTOr): A vectorized molecular mechamics program for biopolymers. Comput. Chem. 16:243-248, 1992.
-
(1992)
Comput. Chem.
, vol.16
, pp. 243-248
-
-
Morikami, K.1
Nakai, T.2
Kidera, M.3
Saito, M.4
Nakamura, H.5
-
71
-
-
0001295503
-
Principal component analysis and long time protein dynamics
-
Balsea, M.A., Wriggers, W. Oono, Y., Schulten, K. Principal component analysis and long time protein dynamics. J. Phys. Chem. 100:2567-2472, 1996.
-
(1996)
J. Phys. Chem.
, vol.100
, pp. 2567-12472
-
-
Balsea, M.A.1
Wriggers, W.2
Oono, Y.3
Schulten, K.4
-
72
-
-
0030068480
-
2 in noncrystalline environments show a subunit transition from the open to the closed conformation
-
2 in noncrystalline environments show a subunit transition from the open to the closed conformation, Protein Sci. 5:62-71, 1996.
-
(1996)
Protein Sci.
, vol.5
, pp. 62-71
-
-
García, A.E.1
Harman, J.G.2
-
73
-
-
0031231987
-
Multi-basin dynamics of a protein in a crystal environment
-
García, A.E., Blumenfeld, R., Hummer, G., Krumhansl, J.A. Multi-basin dynamics of a protein in a crystal environment. Physica D 107:225-239, 1997.
-
(1997)
Physica D
, vol.107
, pp. 225-239
-
-
García, A.E.1
Blumenfeld, R.2
Hummer, G.3
Krumhansl, J.A.4
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