-
1
-
-
0025061676
-
Nucleic-acid structure-tetraloops and RNA folding
-
Uhlenbeck, O. Nucleic-acid structure-tetraloops and RNA folding. Nature 1990, 346, 613-614.
-
(1990)
Nature
, vol.346
, pp. 613-614
-
-
Uhlenbeck, O.1
-
2
-
-
0035256512
-
Important role of the tetraloop region of 4.5S RNA in SRP binding to its receptor FtsY
-
Jagath, J. R.; Matassova, N. B.; de Leeuw, E.; Wernecke, J. M.; Lentzen, G.; Rodnina, M. V.; Luirink, J.; Wintermeyer, W. Important role of the tetraloop region of 4.5S RNA in SRP binding to its receptor FtsY. RNA 2001, 7, 293-301.
-
(2001)
RNA
, vol.7
, pp. 293-301
-
-
Jagath, J.R.1
Matassova, N.B.2
de Leeuw, E.3
Wernecke, J.M.4
Lentzen, G.5
Rodnina, M.V.6
Luirink, J.7
Wintermeyer, W.8
-
3
-
-
0028303640
-
Molecular evolution of SRP cycle components: Functional implications
-
Althoff, S.; Selinger, D.; Wise, J. A. Molecular evolution of SRP cycle components: Functional implications. Nucleic Acids Res. 1994, 22, 1933-1947.
-
(1994)
Nucleic Acids Res
, vol.22
, pp. 1933-1947
-
-
Althoff, S.1
Selinger, D.2
Wise, J.A.3
-
4
-
-
0025942059
-
A thermodynamic study of unusually stable RNA and DNA hairpins
-
Antao, V. P.; Lai, S. Y.; Tinico, I.; Jr.; A thermodynamic study of unusually stable RNA and DNA hairpins. Nucleic Acids Res. 1991, 19, 5901-5905.
-
(1991)
Nucleic Acids Res
, vol.19
, pp. 5901-5905
-
-
Antao, V.P.1
Lai, S.Y.2
Tinico Jr., I.3
-
6
-
-
0026593806
-
Thermodynamic parameters for loop formation in RNA and DNA hairpin tetraloops
-
Antao, V. P.; Tinoco, I., Jr. Thermodynamic parameters for loop formation in RNA and DNA hairpin tetraloops. Nucleic Acids Res. 1992, 20, 819-824.
-
(1992)
Nucleic Acids Res
, vol.20
, pp. 819-824
-
-
Antao, V.P.1
Tinoco Jr., I.2
-
7
-
-
8344253719
-
Folding thermodynamics and kinetics of YNMG RNA hairpins: Specific incorporation of 8-bromoguanosine leads to stabilization by enhancement of the folding rate
-
Proctor, D. J.; Ma, H.; Kierzek, E.; Kierzek, R.; Gruebele, M.; Bevilacqua, P. C. Folding thermodynamics and kinetics of YNMG RNA hairpins: specific incorporation of 8-bromoguanosine leads to stabilization by enhancement of the folding rate. Biochemistry 2004, 43, 14004-14014.
-
(2004)
Biochemistry
, vol.43
, pp. 14004-14014
-
-
Proctor, D.J.1
Ma, H.2
Kierzek, E.3
Kierzek, R.4
Gruebele, M.5
Bevilacqua, P.C.6
-
8
-
-
17144452674
-
NMR spectroscopy of RNA
-
Fürtig, B.; Richter, C.; Wöhnert, J.; Schwalbe, H. NMR spectroscopy of RNA. ChemBioChem 2003, 4, 936-962.
-
(2003)
ChemBioChem
, vol.4
, pp. 936-962
-
-
Fürtig, B.1
Richter, C.2
Wöhnert, J.3
Schwalbe, H.4
-
9
-
-
2942547665
-
Simulation and modeling of nucleic acid structure, dynamics and interactions
-
Cheatham, T. E. III Simulation and modeling of nucleic acid structure, dynamics and interactions. Curr. Opin. Struct. Biol. 2004, 14, 360-367.
-
(2004)
Curr. Opin. Struct. Biol
, vol.14
, pp. 360-367
-
-
Cheatham III, T.E.1
-
10
-
-
36048957757
-
-
Becker, O, MacKerell, A, Jr, Roux, B, Watanabe, M, Eds, Marcel Dekker Inc, New York
-
MacKerell, A., Jr.; Nilsson, L. Nucleic acid simulations, Computational Biochemistry and Biophysics; Becker, O., MacKerell, A., Jr., Roux, B., Watanabe, M., Eds.; Marcel Dekker Inc.: New York, 1999; pp 441-463.
-
(1999)
Nucleic acid simulations, Computational Biochemistry and Biophysics
, pp. 441-463
-
-
MacKerell Jr., A.1
Nilsson, L.2
-
11
-
-
1242347628
-
Theoretical methods for the simulation of nucleic acids
-
Orozco, M.; Perez, A.; Noy, A.; Luque, F. Theoretical methods for the simulation of nucleic acids. Chem. Soc. Rev. 2003, 32, 350-364.
-
(2003)
Chem. Soc. Rev
, vol.32
, pp. 350-364
-
-
Orozco, M.1
Perez, A.2
Noy, A.3
Luque, F.4
-
12
-
-
18744371588
-
Molecular dynamics and protein function
-
Karplus, M.; Kuriyan, J. Molecular dynamics and protein function. Proc. Natl. Acad. Sci. 2005, 102, 6679-6685.
-
(2005)
Proc. Natl. Acad. Sci
, vol.102
, pp. 6679-6685
-
-
Karplus, M.1
Kuriyan, J.2
-
13
-
-
0032466648
-
Continuum solvent studies of the stability of RNA hairpin loops and helices
-
Srinivasan, J.; Miller, J.; Kollman, P.; Case, D. Continuum solvent studies of the stability of RNA hairpin loops and helices. J. Biomol. Struct. Dyn. 1998, 16, 671-682.
-
(1998)
J. Biomol. Struct. Dyn
, vol.16
, pp. 671-682
-
-
Srinivasan, J.1
Miller, J.2
Kollman, P.3
Case, D.4
-
14
-
-
0034646572
-
Experimental and computational studies of the G[UUCG]C RNA tetraloop
-
Williams, D.; Hall, K. Experimental and computational studies of the G[UUCG]C RNA tetraloop. J. Mol. Biol. 2000, 297, 1045-1061.
-
(2000)
J. Mol. Biol
, vol.297
, pp. 1045-1061
-
-
Williams, D.1
Hall, K.2
-
15
-
-
0036297661
-
RNA simulations: Probing hairpin unfolding and the dynamics of a GNRA tetraloop
-
Sorin, E.; Engelhardt, M.; Herschlag, D.; Pande, V. RNA simulations: probing hairpin unfolding and the dynamics of a GNRA tetraloop. J. Mol. Biol. 2002, 317, 493-506.
-
(2002)
J. Mol. Biol
, vol.317
, pp. 493-506
-
-
Sorin, E.1
Engelhardt, M.2
Herschlag, D.3
Pande, V.4
-
16
-
-
0344119523
-
Effects of base substitutions in an RNA hairpin from molecular dynamics and free energy simulations
-
Sarzynska, J.; Nilsson, L.; Kulinski, T. Effects of base substitutions in an RNA hairpin from molecular dynamics and free energy simulations. Biophys. J. 2003, 85, 3445-3459.
-
(2003)
Biophys. J
, vol.85
, pp. 3445-3459
-
-
Sarzynska, J.1
Nilsson, L.2
Kulinski, T.3
-
17
-
-
22144496413
-
Does water play a structural role in the folding of small nucleic acids?
-
Sorin, E.; Rhee, Y.; Pande, V. Does water play a structural role in the folding of small nucleic acids? Biophys. J. 2005, 88, 2516-2524.
-
(2005)
Biophys. J
, vol.88
, pp. 2516-2524
-
-
Sorin, E.1
Rhee, Y.2
Pande, V.3
-
18
-
-
0042845840
-
Insights into Nucleic Acid Conformational Dynamics from Massively Parallel Stochastic Simulations
-
Sorin, E.; Rhee, Y.; Nakatani, B.; Pande, V. Insights into Nucleic Acid Conformational Dynamics from Massively Parallel Stochastic Simulations. Biophys. J. 2003, 85, 790-803.
-
(2003)
Biophys. J
, vol.85
, pp. 790-803
-
-
Sorin, E.1
Rhee, Y.2
Nakatani, B.3
Pande, V.4
-
19
-
-
32644451166
-
Molecular, dynamics simulations of sarcin-ricin rRNA motif
-
Spackova, N.; Sponer, J. Molecular, dynamics simulations of sarcin-ricin rRNA motif. Nucleic Acids Res. 2006, 34, 697-708.
-
(2006)
Nucleic Acids Res
, vol.34
, pp. 697-708
-
-
Spackova, N.1
Sponer, J.2
-
20
-
-
0035700275
-
-
Li, W.; Ma, B.; Shapiro, B. Molecular dynamics simulations of the denaturation and refolding of an RNA tetraloop. 2001, 19, 381-396.
-
(2001)
Molecular dynamics simulations of the denaturation and refolding of an RNA tetraloop
, vol.19
, pp. 381-396
-
-
Li, W.1
Ma, B.2
Shapiro, B.3
-
21
-
-
0033064123
-
Unrestrained Stochastic Dynamics Simulations of the UUCG Tetraloop Using an Implicit Solvation Model
-
Williams, D. J.; Hall, K. B. Unrestrained Stochastic Dynamics Simulations of the UUCG Tetraloop Using an Implicit Solvation Model. Biophys. J. 1999, 76, 3192-3205.
-
(1999)
Biophys. J
, vol.76
, pp. 3192-3205
-
-
Williams, D.J.1
Hall, K.B.2
-
22
-
-
3042734385
-
Molecular dynamics simulations of Guanine quadruplex loops: Advances and force field limitations
-
Fadrna, E.; Spackova, N.; Stefl, R.; Koca, J.; Cheatham, T. E., III; Sponer, J. Molecular dynamics simulations of Guanine quadruplex loops: advances and force field limitations. Biophys. J. 2004, 87, 227-242.
-
(2004)
Biophys. J
, vol.87
, pp. 227-242
-
-
Fadrna, E.1
Spackova, N.2
Stefl, R.3
Koca, J.4
Cheatham III, T.E.5
Sponer, J.6
-
23
-
-
0032560959
-
Continuum solvent studies of the stability of DNA, RNA and phosphoramidate-DNA helices
-
Srinivasan, J.; Cheatham, T. E., III; Cieplak, P.; Kollman, P.; Case, D. Continuum solvent studies of the stability of DNA, RNA and phosphoramidate-DNA helices. J. Am. Chem. Soc. 1998, 120, 9401-9409.
-
(1998)
J. Am. Chem. Soc
, vol.120
, pp. 9401-9409
-
-
Srinivasan, J.1
Cheatham III, T.E.2
Cieplak, P.3
Kollman, P.4
Case, D.5
-
24
-
-
0032556243
-
Free Energy Analysis of the Conformational Stability of A and B Forms of DNA in Solution
-
Jayaram, B.; Sprous, D.; Young, M. A.; Beveridge, D. L. Free Energy Analysis of the Conformational Stability of A and B Forms of DNA in Solution. J. Am. Chem. Soc. 1998, 120, 10629-10633.
-
(1998)
J. Am. Chem. Soc
, vol.120
, pp. 10629-10633
-
-
Jayaram, B.1
Sprous, D.2
Young, M.A.3
Beveridge, D.L.4
-
25
-
-
0034521981
-
Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models
-
Kollman, P. I.; Massova, I.; Reyes, C.; Kuhn, B.; Huo, S.; Chong, L.; Lee, M.; Lee, T.; Duan, Y.; Wang, W.; Donini, O.; Cieplak, P.; Srinivasan, J.; Case, D.; Cheatham, T., III Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Acc. Chem. Res. 2000, 33, 889-897.
-
(2000)
Acc. Chem. Res
, vol.33
, pp. 889-897
-
-
Kollman, P.I.1
Massova, I.2
Reyes, C.3
Kuhn, B.4
Huo, S.5
Chong, L.6
Lee, M.7
Lee, T.8
Duan, Y.9
Wang, W.10
Donini, O.11
Cieplak, P.12
Srinivasan, J.13
Case, D.14
Cheatham III, T.15
-
26
-
-
0347949637
-
Revisiting free energy calculations: A theoretical connection to MM/PBSA and direct calculation of the association free energy
-
Swanson, J.; Henchman, R.; McCammon, J. Revisiting free energy calculations: A theoretical connection to MM/PBSA and direct calculation of the association free energy. Biophys. J. 2004, 86, 67-74.
-
(2004)
Biophys. J
, vol.86
, pp. 67-74
-
-
Swanson, J.1
Henchman, R.2
McCammon, J.3
-
27
-
-
24344456625
-
Study of the insulin dimerization: Binding free energy calculations and perresidue free energy decomposition
-
Zoete, V.; Meuwly, M.; Karplus, M. Study of the insulin dimerization: binding free energy calculations and perresidue free energy decomposition. Proteins 2005, 61, 79-93.
-
(2005)
Proteins
, vol.61
, pp. 79-93
-
-
Zoete, V.1
Meuwly, M.2
Karplus, M.3
-
28
-
-
0347602124
-
Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf
-
Gohlke, H.; Case, D. Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf. J. Comput. Chem. 2004, 25, 238-250.
-
(2004)
J. Comput. Chem
, vol.25
, pp. 238-250
-
-
Gohlke, H.1
Case, D.2
-
29
-
-
0001101548
-
Free Energy Analysis of Protein-DNA Binding: The EcoRI Endonuclease-DNA Complex
-
Jayaram, B.; McConnell, K.; Dixit, S.; Beveridge, D. Free Energy Analysis of Protein-DNA Binding: The EcoRI Endonuclease-DNA Complex. J. Comput. Phys. 1999, 151, 333-357.
-
(1999)
J. Comput. Phys
, vol.151
, pp. 333-357
-
-
Jayaram, B.1
McConnell, K.2
Dixit, S.3
Beveridge, D.4
-
30
-
-
0037442584
-
Molecular Dynamics Simulations and Thermodynamics Analysis of DNA-Drug Complexes. Minor Groove Binding between 4′,6-Diamidino-2-phenylindole and DNA Duplexes in Solution
-
Spackova, N.; Cheatham, T. E., III; Ryjácek, F.; Lankas, F.; van Meervelt, L.; Hobza, P.; Sponer, J. Molecular Dynamics Simulations and Thermodynamics Analysis of DNA-Drug Complexes. Minor Groove Binding between 4′,6-Diamidino-2-phenylindole and DNA Duplexes in Solution. J. Am. Chem. Soc. 2003, 125, 1759-1769.
-
(2003)
J. Am. Chem. Soc
, vol.125
, pp. 1759-1769
-
-
Spackova, N.1
Cheatham III, T.E.2
Ryjácek, F.3
Lankas, F.4
van Meervelt, L.5
Hobza, P.6
Sponer, J.7
-
31
-
-
0037234043
-
Free energy calculations for theophylline binding to an RNA aptamer: Comparison of MM-PBSA and thermodynamic integration methods
-
Gouda, H.; Kuntz, I.; Case, D.; Kollman, P. Free energy calculations for theophylline binding to an RNA aptamer: Comparison of MM-PBSA and thermodynamic integration methods. Biopolymers 2003, 68, 16-34.
-
(2003)
Biopolymers
, vol.68
, pp. 16-34
-
-
Gouda, H.1
Kuntz, I.2
Case, D.3
Kollman, P.4
-
32
-
-
0034212858
-
Free energy analysis of the folding process of villin headpiece subdomain
-
Lee, M.; Duan, Y.; Kollman, P. Free energy analysis of the folding process of villin headpiece subdomain. Proteins 2000, 39, 309-316.
-
(2000)
Proteins
, vol.39
, pp. 309-316
-
-
Lee, M.1
Duan, Y.2
Kollman, P.3
-
33
-
-
0035814387
-
Theoretical studies of d (A:T)-based parallel-stranded DNA duplexes
-
Cubero, E.; Luque, F.; Orozco, M. Theoretical studies of d (A:T)-based parallel-stranded DNA duplexes. J. Am. Chem. Soc. 2001, 123, 12018-12025.
-
(2001)
J. Am. Chem. Soc
, vol.123
, pp. 12018-12025
-
-
Cubero, E.1
Luque, F.2
Orozco, M.3
-
34
-
-
0034625886
-
Nanosecond molecular dynamics of zipper-like DNA duplex structures containing sheared G:A mismatch pairs
-
Spackova, N.; Berger, I.; Sponer, J. Nanosecond molecular dynamics of zipper-like DNA duplex structures containing sheared G:A mismatch pairs. J. Am. Chem. Soc. 2000, 122, 7564-7572.
-
(2000)
J. Am. Chem. Soc
, vol.122
, pp. 7564-7572
-
-
Spackova, N.1
Berger, I.2
Sponer, J.3
-
35
-
-
0141956090
-
Generalized bom model with a simple smoothing function
-
Im, W.; Lee, M. S.; Brooks, C. L., III Generalized bom model with a simple smoothing function. J. Comput. Chem. 2003, 24, 1691-1702.
-
(2003)
J. Comput. Chem
, vol.24
, pp. 1691-1702
-
-
Im, W.1
Lee, M.S.2
Brooks III, C.L.3
-
36
-
-
0037157693
-
-
Lee, M. S.; Salsbury, F. R., Jr.; Brooks, C. L., III Novel generalized Born methods. J. Chem. Phys. 2002, 116, 10606-10614.
-
Lee, M. S.; Salsbury, F. R., Jr.; Brooks, C. L., III Novel generalized Born methods. J. Chem. Phys. 2002, 116, 10606-10614.
-
-
-
-
37
-
-
0029073091
-
The crystal structure of an all-RNA hammerhead ribozyme: A proposed mechanism for RNA catalytic cleavage
-
Scott, W. G.; Finch, J. T.; Klug, A. The crystal structure of an all-RNA hammerhead ribozyme: a proposed mechanism for RNA catalytic cleavage. Cell 1995, 81, 991-1002.
-
(1995)
Cell
, vol.81
, pp. 991-1002
-
-
Scott, W.G.1
Finch, J.T.2
Klug, A.3
-
38
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
Jorgensen, W. L.; Chandrashekhar, J.; Madura, J.; Impey, R. W.; Klein, M. L. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 1983, 79, 926-935.
-
(1983)
J. Chem. Phys
, vol.79
, pp. 926-935
-
-
Jorgensen, W.L.1
Chandrashekhar, J.2
Madura, J.3
Impey, R.W.4
Klein, M.L.5
-
39
-
-
84986512474
-
CHARMM: A program for macromolecular energy, minmimization, and dynamics calculations
-
Brooks, B.; Braccoleri, R.; Olaf son, B.; States, D.; Swaminathan, S.; Karplus, M. CHARMM: A program for macromolecular energy, minmimization, and dynamics calculations. J. Comput. Chem. 1983, 4, 187-217.
-
(1983)
J. Comput. Chem
, vol.4
, pp. 187-217
-
-
Brooks, B.1
Braccoleri, R.2
Olaf son, B.3
States, D.4
Swaminathan, S.5
Karplus, M.6
-
40
-
-
0348244547
-
All atom empirical force field for nucleic acids: 1) Parameter optimization based on small molecule and condensed phase macromolecular target data
-
Foloppe, N.; MacKerell, A. D., Jr. All atom empirical force field for nucleic acids: 1) Parameter optimization based on small molecule and condensed phase macromolecular target data. J. Comput. Chem. 2000, 21, 86-104.
-
(2000)
J. Comput. Chem
, vol.21
, pp. 86-104
-
-
Foloppe, N.1
MacKerell Jr., A.D.2
-
41
-
-
0000214231
-
All-atom empirical force field for nucleic acids: 2) Application to molecular dynamics simulations of DNA and RNA in solution
-
MacKerell, A., Jr.; Banavali, N. All-atom empirical force field for nucleic acids: 2) Application to molecular dynamics simulations of DNA and RNA in solution. J. Comput. Chem. 2000, 21, 105-120.
-
(2000)
J. Comput. Chem
, vol.21
, pp. 105-120
-
-
MacKerell Jr., A.1
Banavali, N.2
-
42
-
-
33645961739
-
A smooth particle mesh Ewald method
-
Essmann, U.; Perera, L.; Berkowitz, M. L.; Darden, T.; Lee, H.; Pedersen, L. A smooth particle mesh Ewald method. J. Chem. Phys. 1995, 103, 8577-8593.
-
(1995)
J. Chem. Phys
, vol.103
, pp. 8577-8593
-
-
Essmann, U.1
Perera, L.2
Berkowitz, M.L.3
Darden, T.4
Lee, H.5
Pedersen, L.6
-
43
-
-
0037168282
-
Atomic radii for continuum electrostatics calculations on nucleic acids
-
Banavali, N. K.; Roux, B. Atomic radii for continuum electrostatics calculations on nucleic acids. J. Phys. Chem. B 2002, 106, 11026-11035.
-
(2002)
J. Phys. Chem. B
, vol.106
, pp. 11026-11035
-
-
Banavali, N.K.1
Roux, B.2
-
45
-
-
0035915354
-
Cooperativity in drug-DNA recognition: A molecular dynamics study
-
Harris, S. A.; Gavathiotis, E.; Searle, M. S.; Orozco, M.; Laughton, C. A. Cooperativity in drug-DNA recognition: a molecular dynamics study. J. Am. Chem. Soc. 2001, 123, 12658-12663.
-
(2001)
J. Am. Chem. Soc
, vol.123
, pp. 12658-12663
-
-
Harris, S.A.1
Gavathiotis, E.2
Searle, M.S.3
Orozco, M.4
Laughton, C.A.5
-
46
-
-
0242585455
-
Configurational entropy and cooperativity between ligand binding and dimerization in glycopeptide antibiotics
-
Jusuf, S.; Loll, P.; Axelsen, P. Configurational entropy and cooperativity between ligand binding and dimerization in glycopeptide antibiotics. J. Am. Chem. Soc. 2003, 125 (13), 3988-3994.
-
(2003)
J. Am. Chem. Soc
, vol.125
, Issue.13
, pp. 3988-3994
-
-
Jusuf, S.1
Loll, P.2
Axelsen, P.3
-
47
-
-
0000127140
-
Method for estimating the configurational entropy of macromolecules
-
Karplus, M.; Kushick, J. N. Method for estimating the configurational entropy of macromolecules. Macromolecules 1981, 14, 325-332.
-
(1981)
Macromolecules
, vol.14
, pp. 325-332
-
-
Karplus, M.1
Kushick, J.N.2
-
48
-
-
0000961995
-
Evaluation of the Configurational entropy for proteins: Application to molecular dynamics simulations of an alpha-helix
-
Levy, R. M.; Karplus, M.; Kushick, J.; Perahia, D. Evaluation of the Configurational entropy for proteins: application to molecular dynamics simulations of an alpha-helix. Macromolecules 1984, 17, 1370-1375.
-
(1984)
Macromolecules
, vol.17
, pp. 1370-1375
-
-
Levy, R.M.1
Karplus, M.2
Kushick, J.3
Perahia, D.4
-
49
-
-
0000885331
-
Harmonic analysis of large systems. I. Methodology
-
Brooks, B. R.; Janezic, D.; Karplus, M. Harmonic analysis of large systems. I. Methodology. J. Comput. Chem. 1995, 16, 1522-1542.
-
(1995)
J. Comput. Chem
, vol.16
, pp. 1522-1542
-
-
Brooks, B.R.1
Janezic, D.2
Karplus, M.3
-
50
-
-
0001351515
-
Estimation of absolute and relative entropies of macromolecules using the covariance matrix
-
Schlitter, J. Estimation of absolute and relative entropies of macromolecules using the covariance matrix. Chem. Phys. Lett. 1993, 215, 617-621.
-
(1993)
Chem. Phys. Lett
, vol.215
, pp. 617-621
-
-
Schlitter, J.1
-
51
-
-
0035828630
-
On the calculation of entropy from covariance matrices of the atomic fluctuations
-
Andricioaei, I.; Karplus, M. On the calculation of entropy from covariance matrices of the atomic fluctuations. J. Chem. Phys. 2001, 115, 6289-6292.
-
(2001)
J. Chem. Phys
, vol.115
, pp. 6289-6292
-
-
Andricioaei, I.1
Karplus, M.2
-
52
-
-
0001064378
-
Free energy determination of polypeptide conformations generated by molecular dynamics
-
Di Nola, A.; Berendsen, H.; Edholm, O. Free energy determination of polypeptide conformations generated by molecular dynamics. Macromolecules 1984, 17, 2044-2050.
-
(1984)
Macromolecules
, vol.17
, pp. 2044-2050
-
-
Di Nola, A.1
Berendsen, H.2
Edholm, O.3
-
53
-
-
25844492293
-
Evaluating the accuracy of the quasiharmonic approximation
-
Chang, C.; Chen, W.; Gilson M. Evaluating the accuracy of the quasiharmonic approximation. J. Chem. Theory Comput. 2005, 1, 1017-1028.
-
(2005)
J. Chem. Theory Comput
, vol.1
, pp. 1017-1028
-
-
Chang, C.1
Chen, W.2
Gilson, M.3
-
54
-
-
0001616080
-
Replica-exchange molecular dynamics method for protein folding
-
Sugita, Y.; Okamoto, Y. Replica-exchange molecular dynamics method for protein folding. Chem. Phys. Lett. 1999, 314, 141-151.
-
(1999)
Chem. Phys. Lett
, vol.314
, pp. 141-151
-
-
Sugita, Y.1
Okamoto, Y.2
-
55
-
-
0033117917
-
New Monte Carlo algorithms for protein folding
-
Hansmann, U. H. E.; Okamoto, Y. New Monte Carlo algorithms for protein folding. Curr. Opin. Struct. Biol. 1999, 9, 177-183.
-
(1999)
Curr. Opin. Struct. Biol
, vol.9
, pp. 177-183
-
-
Hansmann, U.H.E.1
Okamoto, Y.2
-
56
-
-
33646940952
-
Numerical integration of cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
-
Ryckaert, J.-P.; Ciccotti, G.; Berendsen, H. J. C. Numerical integration of cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J. Comput. Phys. 1977, 23, 327-341.
-
(1977)
J. Comput. Phys
, vol.23
, pp. 327-341
-
-
Ryckaert, J.-P.1
Ciccotti, G.2
Berendsen, H.J.C.3
-
57
-
-
34547809547
-
A unified formulation of the constant temperature molecular dynamics methods
-
Nose, S. A unified formulation of the constant temperature molecular dynamics methods. J. Chem. Phys. 1984, 81, 511-519.
-
(1984)
J. Chem. Phys
, vol.81
, pp. 511-519
-
-
Nose, S.1
-
58
-
-
33646178918
-
Calculation of absolute protein-ligand binding affinity using path and endpoint approaches
-
Lee, M. S.; Olson, M. A. Calculation of absolute protein-ligand binding affinity using path and endpoint approaches. Biophys. J. 2006, 90, 864-877.
-
(2006)
Biophys. J
, vol.90
, pp. 864-877
-
-
Lee, M.S.1
Olson, M.A.2
-
59
-
-
84986469420
-
Harmonic analysis of large systems. II. Comparison of different protein models
-
Janezic, D.; Brooks, B. Harmonic analysis of large systems. II. Comparison of different protein models. J. Comput. Chem. 1995, 16, 1543-1553.
-
(1995)
J. Comput. Chem
, vol.16
, pp. 1543-1553
-
-
Janezic, D.1
Brooks, B.2
|