-
1
-
-
15944395860
-
Systematic ab initio gradient calculation of molecular geometries, force constants, and dipole moment derivatives
-
Pulay, P.; Fogarasi, G.; Pang, F.; Boggs, J. E. Systematic ab initio gradient calculation of molecular geometries, force constants, and dipole moment derivatives. J. Am. Chem. Soc. 1979, 101, 2550-2560.
-
(1979)
J. Am. Chem. Soc.
, vol.101
, pp. 2550-2560
-
-
Pulay, P.1
Fogarasi, G.2
Pang, F.3
Boggs, J.E.4
-
2
-
-
6344260593
-
An all-atom empirical energy function for the simulation of nucleic acids
-
MacKerell, A. D., Jr.; Wiorkiewicz-Kuczera, J.; Karplus, M. An all-atom empirical energy function for the simulation of nucleic acids. J. Am. Chem. Soc. 1995, 117, 11946-11975.
-
(1995)
J. Am. Chem. Soc.
, vol.117
, pp. 11946-11975
-
-
MacKerell Jr., A.D.1
Wiorkiewicz-Kuczera, J.2
Karplus, M.3
-
3
-
-
52149120342
-
The importance of multipole moments when describing water and hydrated amino acid cluster geometry
-
Shaik, M.; Devereux, M.; Popelier, P. L. A. The importance of multipole moments when describing water and hydrated amino acid cluster geometry. Mol. Phys. 2008, 106, 1495-1510.
-
(2008)
Mol. Phys.
, vol.106
, pp. 1495-1510
-
-
Shaik, M.1
Devereux, M.2
Popelier, P.L.A.3
-
4
-
-
0029011701
-
A second generation force field for the simulation of proteins, nucleic acids, and organic molecules
-
Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M., Jr.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc. 1995, 117, 5179-5197.
-
(1995)
J. Am. Chem. Soc.
, vol.117
, pp. 5179-5197
-
-
Cornell, W.D.1
Cieplak, P.2
Bayly, C.I.3
Gould, I.R.4
Merz Jr., K.M.5
Ferguson, D.M.6
Spellmeyer, D.C.7
Fox, T.8
Caldwell, J.W.9
Kollman, P.A.10
-
5
-
-
0021757436
-
A new force-field for molecular mechanical simulation of nucleic acids and proteins
-
Weiner, S. J.; Kollman, P. A.; Case, D. A.; Singh, U. C.; Ghio, C.; Alagona, G.; Profeta, S., Jr.; Weiner, P. A new force-field for molecular mechanical simulation of nucleic acids and proteins. J. Am. Chem. Soc. 1984, 106, 765-784.
-
(1984)
J. Am. Chem. Soc.
, vol.106
, pp. 765-784
-
-
Weiner, S.J.1
Kollman, P.A.2
Case, D.A.3
Singh, U.C.4
Ghio, C.5
Alagona, G.6
Profeta Jr., S.7
Weiner, P.8
-
6
-
-
0035974484
-
Molecular mechanical models for organic and biological systems going beyond the atom centered two body additive approximation: Aqueous solution free energies of methanol and N-methyl acetamide, nucleic acid base, and amide hydrogen bonding and chloroform/water partition coefficients of the nucleic acid bases
-
Cieplak, P.; Caldwell, J. W.; Kollman, P. A. Molecular mechanical models for organic and biological systems going beyond the atom centered two body additive approximation: Aqueous solution free energies of methanol and N-methyl acetamide, nucleic acid base, and amide hydrogen bonding and chloroform/water partition coefficients of the nucleic acid bases. J. Comput. Chem. 2001, 22, 1048-1057.
-
(2001)
J. Comput. Chem.
, vol.22
, pp. 1048-1057
-
-
Cieplak, P.1
Caldwell, J.W.2
Kollman, P.A.3
-
8
-
-
0014675222
-
The Refinement of Protein Conformations Using a Macromolecular Energy Minimization Procedure
-
Levitt, M.; Lifson, S. The Refinement of Protein Conformations Using a Macromolecular Energy Minimization Procedure. J. Mol. Biol. 1969, 46, 269-279.
-
(1969)
J. Mol. Biol.
, vol.46
, pp. 269-279
-
-
Levitt, M.1
Lifson, S.2
-
9
-
-
84986512474
-
A program for macromo-lecular energy, minimization and dynamics calculations
-
Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. CHARMM: a program for macromo-lecular energy, minimization and dynamics calculations. J. Comput. Chem. 1983, 4, 187-217.
-
(1983)
J. Comput. Chem.
, vol.4
, pp. 187-217
-
-
Brooks, B.R.1
Bruccoleri, R.E.2
Olafson, B.D.3
States, D.J.4
Swaminathan, S.5
Charmm, K.M.6
-
10
-
-
0000999989
-
Combined Ab initio/empirical approach for optimization of lennard jones parameters
-
Yin, D.; MacKerell, A. D., Jr. Combined Ab Initio/Empirical Approach for Optimization of Lennard Jones Parameters. J. Comput. Chem. 1997, 19, 334-348.
-
(1997)
J. Comput. Chem.
, vol.19
, pp. 334-348
-
-
Yin, D.1
MacKerell Jr., A.D.2
-
11
-
-
14844330742
-
AFMM: A molecular mechanics force field vibrational parametrization program
-
Vaiana, A. C.; Cournia, Z.; Costescu, I. B.; Smith, J. C. AFMM: A molecular mechanics force field vibrational parametrization program. Comput. Phys. Commun. 2005, 167, 34-42.
-
(2005)
Comput. Phys. Commun.
, vol.167
, pp. 34-42
-
-
Vaiana, A.C.1
Cournia, Z.2
Costescu, I.B.3
Smith, J.C.4
-
12
-
-
34147116967
-
Automated Parametrization of Biomolecular Force Fields from Quantum Mechanics/Molecular Mechanics (QM/MM) Simulations through Force Matching
-
Maurer, P.; Laio, A.; Hugosson, H. W.; Colombo, M. C.; Rothlisberger, U. Automated Parametrization of Biomolecular Force Fields from Quantum Mechanics/Molecular Mechanics (QM/MM) Simulations through Force Matching. J. Chem. Theo. Comp. 2007, 3, 628-639.
-
(2007)
J. Chem. Theo. Comp.
, vol.3
, pp. 628-639
-
-
Maurer, P.1
Laio, A.2
Hugosson, H.W.3
Colombo, M.C.4
Rothlisberger, U.5
-
13
-
-
47249094074
-
Automated conformational energy fitting for force-field development
-
Guvench, O.; MacKerell, A. D., Jr. Automated Conformational Energy Fitting for Force-Field Development. J. Mol. Model. 2008, 14, 667-679.
-
(2008)
J. Mol. Model.
, vol.14
, pp. 667-679
-
-
Guvench, O.1
MacKerell Jr., A.D.2
-
14
-
-
77949860182
-
-
(DFF); Aeon Technology Inc.: San Diego, CA
-
DirectForceField (DFF); Aeon Technology Inc.: San Diego, CA, 2006.
-
(2006)
DirectForceField
-
-
-
15
-
-
33645858780
-
Quantum and statistical mechanics studies of liquids. 10. Transferable intermolecular potential functions for water, alcohols, and ethers - Application to liquid water
-
Jorgensen, W. L. Quantum and statistical mechanics studies of liquids. 10. Transferable intermolecular potential functions for water, alcohols, and ethers - application to liquid water. J. Am. Chem. Soc. 1981, 103, 335-340.
-
(1981)
J. Am. Chem. Soc.
, vol.103
, pp. 335-340
-
-
Jorgensen, W.L.1
-
17
-
-
0031547902
-
I-NoLLS: A program for interactive nonlinear least-squares fitting of the parameters of physical models
-
Law, M.; Hutson, J. I-NoLLS: a program for interactive nonlinear least-squares fitting of the parameters of physical models. Comput. Phys. Commun. 1997, 102, 252-268.
-
(1997)
Comput. Phys. Commun.
, vol.102
, pp. 252-268
-
-
Law, M.1
Hutson, J.2
-
18
-
-
0041784950
-
All-atom empirical potential for molecular modeling and dynamics studies of proteins
-
MacKerell, A. D., Jr.; et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B 1998, 102, 3586-3616.
-
(1998)
J. Phys. Chem. B
, vol.102
, pp. 3586-3616
-
-
MacKerell Jr., A.D.1
-
19
-
-
0023042853
-
X-ray Structure and Refinement of Carbonmonoxy (Fe II)-Myoglobin at 1.5 Angstrom Resolution
-
Kuriyan, J.; Wilz, S.; Karplus, M.; Petsko, G. A. X-ray Structure and Refinement of Carbonmonoxy (Fe II)-Myoglobin at 1.5 Angstrom Resolution. J. Mol. Biol. 1986, 192, 133-154.
-
(1986)
J. Mol. Biol.
, vol.192
, pp. 133-154
-
-
Kuriyan, J.1
Wilz, S.2
Karplus, M.3
Petsko, G.A.4
-
20
-
-
36749119973
-
Deformable stochastic boundaries in molecular-dynamics
-
Brooks, C. L.; Karplus, M. Deformable stochastic boundaries in molecular-dynamics. J. Chem. Phys. 1983, 79, 6312-6325.
-
(1983)
J. Chem. Phys.
, vol.79
, pp. 6312-6325
-
-
Brooks, C.L.1
Karplus, M.2
-
21
-
-
84946450438
-
Algorithms for Macro-molecular Dynamics and Constraint Dynamics
-
Van Gunsteren, W. V.; Berendsen, H. J. C. Algorithms for Macro-molecular Dynamics and Constraint Dynamics. Mol. Phys. 1977, 34, 1311-1327.
-
(1977)
Mol. Phys.
, vol.34
, pp. 1311-1327
-
-
Van Gunsteren, W.V.1
Berendsen, H.J.C.2
-
22
-
-
70349509726
-
Anharmonic coupling in molecular dynamics simulations of ligand vibrational relaxation in bound carbonmonoxy myoglobin
-
Devereux, M.; Meuwly, M. Anharmonic Coupling in Molecular Dynamics Simulations of Ligand Vibrational Relaxation in Bound Carbonmonoxy Myoglobin. J. Phys. Chem. B 2009, 13061-13070.
-
(2009)
J. Phys. Chem. B
, pp. 13061-13070
-
-
Devereux, M.1
Meuwly, M.2
-
23
-
-
0000965864
-
Vibrational relaxation of the CO stretch vibration in hemoglobin-CO, myoglobin-CO, and protoheme-CO
-
Owrutsky, J. C.; Li, M.; Locke, B.; Hochstrasser, R. M. Vibrational relaxation of the CO stretch vibration in hemoglobin-CO, myoglobin-CO, and protoheme-CO. J. Phys. Chem. 1995, 99, 4842-4846.
-
(1995)
J. Phys. Chem.
, vol.99
, pp. 4842-4846
-
-
Owrutsky, J.C.1
Li, M.2
Locke, B.3
Hochstrasser, R.M.4
-
24
-
-
0001479606
-
Fast vibrational relaxation for a dipolar molecule in a polar solvent
-
Whitnell, R. M.; Wilson, K. R.; Hynes, J. T. Fast vibrational relaxation for a dipolar molecule in a polar solvent. J. Phys. Chem. 1990, 94, 8625-8628.
-
(1990)
J. Phys. Chem.
, vol.94
, pp. 8625-8628
-
-
Whitnell, R.M.1
Wilson, K.R.2
Hynes, J.T.3
-
25
-
-
0042322523
-
Vibrational energy frequency shifts and relaxation rates for a selected vibrational mode in cytochrome c
-
Bu, L.; Straub, J. E. Vibrational energy frequency shifts and relaxation rates for a selected vibrational mode in cytochrome c. Biophys. J. 2003, 85, 1429-1439.
-
(2003)
Biophys. J.
, vol.85
, pp. 1429-1439
-
-
Bu, L.1
Straub, J.E.2
-
29
-
-
0000873069
-
A Method for the Solution of Certain Non-Linear Problems in Least Squares
-
Levenberg, K. A Method for the Solution of Certain Non-Linear Problems in Least Squares. Q. Appl. Math. 1944, 2, 164-168.
-
(1944)
Q. Appl. Math.
, vol.2
, pp. 164-168
-
-
Levenberg, K.1
-
30
-
-
0000169232
-
An Algorithm for Least-Squares Estimation of Nonlinear Parameters
-
Marquardt, D. An Algorithm for Least-Squares Estimation of Nonlinear Parameters. SIAM J. Appl. Math. 1963, 11, 431-441.
-
(1963)
SIAM J. Appl. Math.
, vol.11
, pp. 431-441
-
-
Marquardt, D.1
-
32
-
-
0035756040
-
Ultrafast dynamics of Myoglobin probed by time-resolved Resonance Raman Spectroscopy
-
Mizutani, Y.; Kitagawa, T. Ultrafast dynamics of Myoglobin probed by time-resolved Resonance Raman Spectroscopy. Chem. Rec. 2001, 1, 258-275.
-
(2001)
Chem. Rec.
, vol.1
, pp. 258-275
-
-
Mizutani, Y.1
Kitagawa, T.2
-
33
-
-
0023234106
-
Rebinding and relaxation in the myoglobin pocket
-
Ansari, A.; Berendzen, J.; Braunstein, D.; Cowen, B. R.; Frauenfelder, H.; Kyung Hong, M.; Iben, I. E. T.; Johnson, J. B.; Ormos, P.; Sauke, T. B.; Scholl, R.; Schulte, A.; Steinbach, P. J.; Vittitow, J. Rebinding and relaxation in the myoglobin pocket. Biophys. Chem. 1987, 26, 337-355.
-
(1987)
Biophys. Chem.
, vol.26
, pp. 337-355
-
-
Ansari, A.1
Berendzen, J.2
Braunstein, D.3
Cowen, B.R.4
Frauenfelder, H.5
Kyung Hong, M.6
Iben, I.E.T.7
Johnson, J.B.8
Ormos, P.9
Sauke, T.B.10
Scholl, R.11
Schulte, A.12
Steinbach, P.J.13
Vittitow, J.14
-
34
-
-
34250350472
-
Quantitative vibrational dynamics of Iron in Carbonyl porphyrins
-
Leu, B. M.; Silvernail, N. J.; Zgierski, M. Z.; Wyllie, G. R. A.; Ellison, M. K.; Scheidt, W. R.; Zhao, J.; Sturhahn, W.; Alp, E. E.; Sage, J. T. Quantitative vibrational dynamics of Iron in Carbonyl porphyrins. Biophys. J. 2007, 92, 3764-3783.
-
(2007)
Biophys. J.
, vol.92
, pp. 3764-3783
-
-
Leu, B.M.1
Silvernail, N.J.2
Zgierski, M.Z.3
Wyllie, G.R.A.4
Ellison, M.K.5
Scheidt, W.R.6
Zhao, J.7
Sturhahn, W.8
Alp, E.E.9
Sage, J.T.10
-
35
-
-
0345973734
-
Vibrational energy relaxation of the cyanide ion in water
-
Hamm, P.; Lim, M.; Hochstrasser, R. M. Vibrational energy relaxation of the cyanide ion in water. J. Chem. Phys. 1997, 107, 10523-10531.
-
(1997)
J. Chem. Phys.
, vol.107
, pp. 10523-10531
-
-
Hamm, P.1
Lim, M.2
Hochstrasser, R.M.3
-
36
-
-
0032517714
-
Non-Markovian Dynamics of the Vibrations of Ions in Water from Femtosecond Infrared Three-Pulse Photon Echoes
-
Hamm, P.; Lim, M.; Hochstrasser, R. M. Non-Markovian Dynamics of the Vibrations of Ions in Water from Femtosecond Infrared Three-Pulse Photon Echoes. Phys. Rev. Lett. 1998, 81, 5326-5329.
-
(1998)
Phys. Rev. Lett.
, vol.81
, pp. 5326-5329
-
-
Hamm, P.1
Lim, M.2
Hochstrasser, R.M.3
-
37
-
-
22944442956
-
Vibrational spectra from atomic fluctuations in dynamics simulations. II. Solvent-induced frequency fluctuations at femtosecond time resolution
-
Schmitz, M.; Tavan, P. Vibrational spectra from atomic fluctuations in dynamics simulations. II. Solvent-induced frequency fluctuations at femtosecond time resolution. J. Chem. Phys. 2004, 121, 12247-12258.
-
(2004)
J. Chem. Phys.
, vol.121
, pp. 12247-12258
-
-
Schmitz, M.1
Tavan, P.2
-
38
-
-
63549100665
-
Classical Simulation of Quantum Energy Flow in Biomol-ecules
-
Stock, G. Classical Simulation of Quantum Energy Flow in Biomol-ecules. Phys. Rev. Lett. 2009, 102, 118301-118304.
-
(2009)
Phys. Rev. Lett.
, vol.102
, pp. 118301-118304
-
-
Stock, G.1
-
39
-
-
58149265267
-
Direct comparison of experimental and calculated NMR- Scalar coupling constants for force field validation and adaptation
-
Schmid, F. F. F.; Meuwly, M. Direct Comparison of Experimental and Calculated NMR- Scalar Coupling Constants for Force Field Validation and Adaptation. J. Chem. Theo. Comp. 2008, 4, 1949-1958.
-
(2008)
J. Chem. Theo. Comp.
, vol.4
, pp. 1949-1958
-
-
Schmid, F.F.F.1
Meuwly, M.2
-
40
-
-
0037123224
-
1H chemical shifts in the hydrogen bonding regions of proteins
-
1H Chemical Shifts in the Hydrogen Bonding Regions of Proteins. J. Am. Chem. Soc. 2002, 124, 4158-4168.
-
(2002)
J. Am. Chem. Soc.
, vol.124
, pp. 4158-4168
-
-
Barfield, M.1
|