-
4
-
-
0025938315
-
Protein Dynamics-Comparison of Simulations with Inelastic neutron Scattering Experiments
-
(1991)
Quart Rev Biophys
, vol.24
, pp. 227-291
-
-
Smith1
-
5
-
-
0027182659
-
The Molecular Force Field of Guanine and its Deuterated Species as Determined from Neutron Ineleastic Scattering and Resonance Raman Measurement
-
of special interest, This paper along with [6•] proposes a detailed interpretation of out-of-plane vibrational motions in purines based a combined analysis of neutron inelastic scattering and infrared and Raman spectra.
-
(1993)
Eur J Biophys
, vol.22
, pp. 225-236
-
-
Dhaouadi1
Ghomi2
Coulombeau3
Coulombeau4
Jobic5
Mojze6
Chinsky7
Turpin8
-
9
-
-
0022419152
-
Protein Mormal-mode Dynamics: Trypsin inhibitor, Crambin, Ribonuclease and Lysozyme
-
(1985)
J Mol Biol
, vol.181
, pp. 423-447
-
-
Levitt1
Sander2
Stern3
-
10
-
-
0026941774
-
Analyzing the Normal Mode Dynamics of Macromolecules by the Component Synthesis Method
-
of special interest, This paper along with [11•] describes a matrix partitioning scheme that should extend the size of molecules for which accurate low-frequency modes can be determined.
-
(1992)
Biopolymers
, vol.32
, pp. 1393-1405
-
-
Hao1
Harvey2
-
11
-
-
84914786577
-
analyzing the Normal Mode Dynamics of Macromolecules by the Component Synthesis Method: Residue Clustering and Multiple-Component Approach
-
of special interest, in press, Extends [10•] above, and reports applications to crambin.
-
(1993)
Biopolymers
-
-
Hao1
Scheraga2
-
13
-
-
0000998079
-
The Effects of Solvent on the Conformation and the Collective Motions of Protein: Normal Mode Analysis and Molecular Dynamics Simulations of Melittin in Water and in Vacuum
-
(1991)
Chem Phys
, vol.158
, pp. 447-472
-
-
Kitao1
Hirata2
Gö3
-
14
-
-
0025292904
-
Langevin Modes of Macromolecules: Application to Crambin and DNA Hammers
-
(1990)
Biopolymers
, vol.29
, pp. 1409-1421
-
-
Kottalam1
Case2
-
16
-
-
2442460927
-
Molecular Dynamics Analysis of NMR Relaxation in a Zinc-Finger Peptide
-
of special interest, This paper compares normal mode and molecular dynamics predictions for a variety of spin-relaxation parameters.
-
(1992)
J Am Chem Soc
, vol.114
, pp. 9059-9067
-
-
Palmer1
Case2
-
18
-
-
0025066772
-
Normal Mode Analysis of Human Lysozyme: Study of the Relative Motion of the Two Domains and Characterization of the Harmonic Motion
-
(1990)
Proteins
, vol.8
, pp. 258-279
-
-
Gibrat1
Gö2
-
19
-
-
0025753631
-
Projection of Monte Carlo and Molecular Dynamics Trajectories onto the Normal Mode Axes: Human Lysozyme
-
(1991)
Proteins
, vol.10
, pp. 106-116
-
-
Horiuchi1
Gö2
-
20
-
-
0027511431
-
Normal Mode Analysis of G-Actin
-
of special interest, the soft vibrational modes of G-actin are found to twist about the phosphate-binding loops and an opening of the ADP-binding cleft.
-
(1993)
J Mol Biol
, vol.230
, pp. 186-195
-
-
Tirion1
Ben-Avraham2
-
21
-
-
0027186150
-
Normal Mode Analysis of Mouse Epidermal Growth Factor: Characterization of the Harmonic Motion
-
of special interest, Describes a ‘hinge-bending’ mode between a nearly rigid amino-terminal segment and a carboxy-terminal domain that consists approximately of three rigid segments.
-
(1993)
Proteins
, vol.16
, pp. 423-436
-
-
Ikura1
Gö2
-
22
-
-
0027161809
-
Picosecond Timescale Rigid-Helix and Side-Chain motions in Deoxymyoglobin
-
of special interest, Discusses ways in which molecular dynamics simulations can be analyzed in terms of quasi rigid-body dynamics.
-
(1993)
Proteins
, vol.16
, pp. 141-154
-
-
Furois-Corbin1
Smith2
Kneller3
-
23
-
-
0027179514
-
Conformational Deformation in Deoxymyoglobin by Hydrostatic Pressure
-
of special interest, This study uses normal modes and a strain tensor analysis to compute volume fluctuations and compressibility of myoglobin at pressures up to 1000 atmospheres.
-
(1993)
Proteins
, vol.16
, pp. 327-340
-
-
Yamato1
Higo2
Seno3
Gö4
-
25
-
-
0000118827
-
Harmonic and Quasiharmonic Dynamics of Crambin
-
(1990)
J Phys Chem
, vol.94
, pp. 8091-8097
-
-
Teeter1
Case2
-
28
-
-
0027390460
-
The Contribution of Cross-Links to Protein Stability — a Normal Mode Analysis of the Configurational Entropy of the Native State
-
-1 at 300 K, and that this change is comparable to the entropy loss in the unfolded state.
-
(1993)
Proteins
, vol.15
, pp. 71-79
-
-
Tidor1
Karplus2
-
30
-
-
0023512803
-
Anisotropy and Anharmonicity of Atomic Fluctuations in Proteins: Analysis of a Molecular Dynamics Simulation
-
(1987)
Proteins
, vol.2
, pp. 236-259
-
-
Ichiye1
Karplus2
-
31
-
-
0000577041
-
Large-Amplitude Nonlinear Motions in Proteins
-
of special interest, This study analyzes dynamic fluctuations by projecting motions found in a simulation of crambin onto principal axes defined in a quasiharmonic manner.
-
(1992)
Physical Review Letters
, vol.68
, pp. 2696-2699
-
-
García1
-
32
-
-
0000078369
-
Effects of Solvent on the Conformation and the Collective Motions of a Protein. 3. Free Energy Analysis by the Extended RISM Theory
-
of special interest, The extended RISM integral equation theory is used to evaluate Solvation contributions to the energy profile along low-frequency normal mode directions.
-
(1993)
J Phys Chem
, vol.97
, pp. 10231-10235
-
-
Kitao1
Hirata2
Gö3
-
33
-
-
0023053635
-
Effect of Anisotropy and Anharmonicity on PAein Crystallographic Refinements. An Evaluation by Molecular Dynamics
-
(1986)
J Mol Biol
, vol.190
, pp. 227-254
-
-
Kuriyan1
Petsko2
Levy3
Karplus4
-
34
-
-
0022372682
-
Do Vibrational Spectroscopies Uniquely Describe Protein Dynamics? The Case for myoglobin
-
(1985)
Biophys J
, vol.48
, pp. 1027-1044
-
-
Bialek1
Goldstein2
-
35
-
-
4243788456
-
Temperature Echoes in Molecular Dynamics Simulations of Proteins
-
of outstanding interest, A novel computational procedure that applies instantaneous temperature ‘quenches’ during molecular dynamics simulations, is illustrated with calculations on bovine pancreatic trypsin inhibitor (BPTI).
-
(1993)
Phys Rev Lett
, vol.70
, pp. 3514-3517
-
-
Becker1
Karplus2
-
36
-
-
0042091834
-
Packing Structures and Transitions in Liquids and Solids
-
(1984)
Science
, vol.225
, pp. 983-989
-
-
Stillinger1
Weber2
-
38
-
-
0027641567
-
Computer Simulations of the Flexibility of a Series of Synthetic Cyclic Peptide Analogues
-
of outstanding interest, Compares normal mode and molecular dynamics simulations for a series of peptide analogues that differ in the extent to which chemical constraints limit atomic fluctuations.
-
(1993)
Biopolymers
, vol.33
, pp. 1249-1270
-
-
Thomas1
Roux2
Smith3
-
42
-
-
0027402494
-
Exploring the Energy Landscape in Proteins
-
of outstanding interest, This work estimates the fraction of unstable normal modes in a protein, and connects this to the distribution of barrier heights between conformational substates.
-
(1993)
Proc Natl Acad Scad USA
, vol.90
, pp. 809-813
-
-
Straub1
Thirumalai2
-
44
-
-
0026663419
-
Normal Mode Refinement: Crystallographic Refinement of Protein Dynamic Structure. I. Theory and Test by Simulated Diffraction Data
-
of special interest, Describes a method to expand the Debye-Waller factor in terms of low-frequency normal modes, whose amplitudes and directions are optimized in the process of crystallographic refinement.
-
(1992)
J Mol Biol
, vol.225
, pp. 457-475
-
-
Kidera1
Gö2
-
45
-
-
0026717834
-
Normal Mode Refinement: Crystallographic Refinement of Protein Dynamic Structure. II. Application to Human Lysozyme
-
of special interest, Shows that the optimized modes in lysozyme bear a strong resemblance to the original normal modes.
-
(1992)
J Mol Biol
, vol.225
, pp. 477-486
-
-
Kidera1
Inaka2
Matsushima3
Gö4
-
46
-
-
0026592954
-
Correlations of Atomic Movements in Lysozyme Crystals
-
of special interest, This study analyzes diffuse scattering data in two crystalline forms of lysozyme, concluding that the principal component of atomic movement, responsible for more than 90% of the mean-square displacement, has a liquid-like character, with short-range correlations that decay after a few atomic coordination shells.
-
(1992)
Proteins
, vol.12
, pp. 145-157
-
-
Clarage1
Clarage2
Phillips3
Sweet4
Caspar5
-
47
-
-
0027866244
-
Combination of Neutron Scattering and Molecular Dynamics to Determine Internal Motions in Biomolecules
-
(1993)
Mol Simul
, vol.10
, pp. 363-375
-
-
Smith1
Kneller2
-
50
-
-
0000279972
-
Influence of Vibrational Motion on Solid State Line Shapes and NMR Relaxation
-
(1985)
J Chem Phys
, vol.82
, pp. 4753-4761
-
-
Henry1
Szabo2
-
52
-
-
0001232562
-
A Collective NMR Relaxation Model Applied to Protein Dynamics
-
of special interest, Applies a model similar to that described in [44•] to the NMR structure refinement problem.
-
(1994)
Physical Review Letters
, vol.72
, pp. 940-943
-
-
Brüschweiler1
Case2
-
53
-
-
0027732618
-
Effect of Solvent on Collective Motions in Globular Protein
-
of outstanding interest, Analyzes the results of molecular dynamics simulations on bovine pancreatic trypsn inhibitor in terms of principal components of the covariance matrix of positionl fluctuation, with particular attention to the effects of solvent damping on low-frequency effective modes.
-
(1993)
J Mol Biol
, vol.234
, pp. 1207-1217
-
-
Hayward1
Kitao2
Hirata3
Gö4
-
54
-
-
0027441950
-
Essential Dynamics of Proteins
-
of outstanding interest, Analyzes the results of molecular dynamics simulations of lysozyme in terms of eigenvectors of the covariance matrix of positional fluctuations. Anharmonic behaviour appears to be restricted to a relatively small ‘essential subspace’.
-
(1993)
Proteins
, vol.17
, pp. 412-425
-
-
Amadei1
Linssen2
Berendsen3
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