-
1
-
-
84861367246
-
Biomolecular Simulation: A Computational Microscope for Molecular Biology
-
Dror, R. O.; Dirks, R. M.; Grossman, J. P.; Xu, H. F.; Shaw, D. E. Biomolecular Simulation: A Computational Microscope for Molecular Biology Annu. Rev. Biophys. 2012, 41, 429-452
-
(2012)
Annu. Rev. Biophys.
, vol.41
, pp. 429-452
-
-
Dror, R.O.1
Dirks, R.M.2
Grossman, J.P.3
Xu, H.F.4
Shaw, D.E.5
-
2
-
-
84892963298
-
Assessing the Accuracy of Physical Models Used in Protein-Folding Simulations: Quantitative Evidence from Long Molecular Dynamics Simulations
-
Piana, S.; Klepeis, J. L.; Shaw, D. E. Assessing the Accuracy of Physical Models Used in Protein-Folding Simulations: Quantitative Evidence from Long Molecular Dynamics Simulations Curr. Opin. Struct. Biol. 2014, 24, 98-105
-
(2014)
Curr. Opin. Struct. Biol.
, vol.24
, pp. 98-105
-
-
Piana, S.1
Klepeis, J.L.2
Shaw, D.E.3
-
3
-
-
33846314325
-
Force Field Effects on a Beta-Sheet Protein Domain Structure in Thermal Unfolding Simulations
-
Wang, T.; Wade, R. C. Force Field Effects on a Beta-Sheet Protein Domain Structure in Thermal Unfolding Simulations J. Chem. Theory Comput. 2006, 2, 140-148
-
(2006)
J. Chem. Theory Comput.
, vol.2
, pp. 140-148
-
-
Wang, T.1
Wade, R.C.2
-
4
-
-
67650359927
-
Force Field Bias in Protein Folding Simulations
-
Freddolino, P. L.; Park, S.; Roux, B.; Schulten, K. Force Field Bias in Protein Folding Simulations Biophys. J. 2009, 96, 3772-3780
-
(2009)
Biophys. J.
, vol.96
, pp. 3772-3780
-
-
Freddolino, P.L.1
Park, S.2
Roux, B.3
Schulten, K.4
-
5
-
-
46749127364
-
Are Current Molecular Dynamics Force Fields Too Helical?
-
Best, R. B.; Buchete, N. V.; Hummer, G. Are Current Molecular Dynamics Force Fields Too Helical? Biophys. J. 2008, 95, L7-L9
-
(2008)
Biophys. J.
, vol.95
, pp. 7-L9
-
-
Best, R.B.1
Buchete, N.V.2
Hummer, G.3
-
6
-
-
79954518426
-
Optimizing Protein-Solvent Force Fields to Reproduce Intrinsic Conformational Preferences of Model Peptides
-
Nerenberg, P. S.; Head-Gordon, T. Optimizing Protein-Solvent Force Fields to Reproduce Intrinsic Conformational Preferences of Model Peptides J. Chem. Theory Comput. 2011, 7, 1220-1230
-
(2011)
J. Chem. Theory Comput.
, vol.7
, pp. 1220-1230
-
-
Nerenberg, P.S.1
Head-Gordon, T.2
-
7
-
-
77953513118
-
Improved Side-Chain Torsion Potentials for the Amber ff99SB Protein Force Field
-
Lindorff-Larsen, K.; Piana, S.; Palmo, K.; Maragakis, P.; Klepeis, J. L.; Dror, R. O.; Shaw, D. E. Improved Side-Chain Torsion Potentials for the Amber ff99SB Protein Force Field Proteins 2010, 78, 1950-1958
-
(2010)
Proteins
, vol.78
, pp. 1950-1958
-
-
Lindorff-Larsen, K.1
Piana, S.2
Palmo, K.3
Maragakis, P.4
Klepeis, J.L.5
Dror, R.O.6
Shaw, D.E.7
-
8
-
-
77956606590
-
NMR-Based Protein Potentials
-
Li, D. W.; Bruschweiler, R. NMR-Based Protein Potentials Angew. Chem., Int. Ed. 2010, 49, 6778-6780
-
(2010)
Angew. Chem., Int. Ed.
, vol.49
, pp. 6778-6780
-
-
Li, D.W.1
Bruschweiler, R.2
-
9
-
-
67649494492
-
Optimized Molecular Dynamics Force Fields Applied to the Helix-Coil Transition of Polypeptides
-
Best, R. B.; Hummer, G. Optimized Molecular Dynamics Force Fields Applied to the Helix-Coil Transition of Polypeptides J. Phys. Chem. B 2009, 113, 9004-9015
-
(2009)
J. Phys. Chem. B
, vol.113
, pp. 9004-9015
-
-
Best, R.B.1
Hummer, G.2
-
10
-
-
84863775602
-
Refinement of Protein Structure Homology Models via Long, All-Atom Molecular Dynamics Simulations
-
Raval, A.; Piana, S.; Eastwood, M. P.; Dror, R. O.; Shaw, D. E. Refinement of Protein Structure Homology Models via Long, All-Atom Molecular Dynamics Simulations Proteins 2012, 80, 2071-2079
-
(2012)
Proteins
, vol.80
, pp. 2071-2079
-
-
Raval, A.1
Piana, S.2
Eastwood, M.P.3
Dror, R.O.4
Shaw, D.E.5
-
11
-
-
84924375346
-
Molecular Dynamics Simulations of 441 Two-Residue Peptides in Aqueous Solution: Conformational Preferences and Neighboring Residue Effects with the Amber ff99SB-ildn-NMR Force Field
-
Li, S.; Andrews, C. T.; Frembgen-Kesner, T.; Miller, M. S.; Siemonsma, S. L.; Collingsworth, T. D.; Rockafellow, I. T.; Ngo, N. A.; Campbell, B. A.; Brown, R. F.; Guo, C.; Schrodt, M.; Liu, Y.-T.; Elcock, A. H. Molecular Dynamics Simulations of 441 Two-Residue Peptides in Aqueous Solution: Conformational Preferences and Neighboring Residue Effects with the Amber ff99SB-ildn-NMR Force Field J. Chem. Theory Comput. 2015, 11, 1315-1329
-
(2015)
J. Chem. Theory Comput.
, vol.11
, pp. 1315-1329
-
-
Li, S.1
Andrews, C.T.2
Frembgen-Kesner, T.3
Miller, M.S.4
Siemonsma, S.L.5
Collingsworth, T.D.6
Rockafellow, I.T.7
Ngo, N.A.8
Campbell, B.A.9
Brown, R.F.10
Guo, C.11
Schrodt, M.12
Liu, Y.-T.13
Elcock, A.H.14
-
12
-
-
33846783019
-
Structure and Dynamics of the Homologous Series of Alanine Peptides: A Joint Molecular Dynamics/NMR Study
-
Graf, J.; Nguyen, P. H.; Stock, G.; Schwalbe, H. Structure and Dynamics of the Homologous Series of Alanine Peptides: A Joint Molecular Dynamics/NMR Study J. Am. Chem. Soc. 2007, 129, 1179-1189
-
(2007)
J. Am. Chem. Soc.
, vol.129
, pp. 1179-1189
-
-
Graf, J.1
Nguyen, P.H.2
Stock, G.3
Schwalbe, H.4
-
13
-
-
84906937237
-
Neighboring Residue Effects in Terminally Blocked Dipeptides: Implications for Residual Secondary Structures in Intrinsically Unfolded/Disordered Proteins
-
Jung, Y. S.; Oh, K. I.; Hwang, G. S.; Cho, M. Neighboring Residue Effects in Terminally Blocked Dipeptides: Implications for Residual Secondary Structures in Intrinsically Unfolded/Disordered Proteins Chirality 2014, 26, 443-452
-
(2014)
Chirality
, vol.26
, pp. 443-452
-
-
Jung, Y.S.1
Oh, K.I.2
Hwang, G.S.3
Cho, M.4
-
14
-
-
84859611714
-
Are Protein Force Fields Getting Better? A Systematic Benchmark on 524 Diverse NMR Measurements
-
Beauchamp, K. A.; Lin, Y.-S.; Das, R.; Pande, V. S. Are Protein Force Fields Getting Better? A Systematic Benchmark on 524 Diverse NMR Measurements J. Chem. Theory Comput. 2012, 8, 1409-1414
-
(2012)
J. Chem. Theory Comput.
, vol.8
, pp. 1409-1414
-
-
Beauchamp, K.A.1
Lin, Y.-S.2
Das, R.3
Pande, V.S.4
-
15
-
-
33748518255
-
Comparison of Multiple Amber Force Fields and Development of Improved Protein Backbone Parameters
-
Hornak, V.; Abel, R.; Okur, A.; Strockbine, B.; Roitberg, A.; Simmerling, C. Comparison of Multiple Amber Force Fields and Development of Improved Protein Backbone Parameters Proteins 2006, 65, 712-725
-
(2006)
Proteins
, vol.65
, pp. 712-725
-
-
Hornak, V.1
Abel, R.2
Okur, A.3
Strockbine, B.4
Roitberg, A.5
Simmerling, C.6
-
16
-
-
84921508413
-
Residue-Specific Force Field Based on Protein Coil Library. RSFF2: Modification of AMBER ff99SB
-
Zhou, C.-Y.; Jiang, F.; Wu, Y.-D. Residue-Specific Force Field Based on Protein Coil Library. RSFF2: Modification of AMBER ff99SB J. Phys. Chem. B 2015, 119, 1035-1047
-
(2015)
J. Phys. Chem. B
, vol.119
, pp. 1035-1047
-
-
Zhou, C.-Y.1
Jiang, F.2
Wu, Y.-D.3
-
17
-
-
0004016501
-
Comparison of Simple Potential Functions for Simulating Liquid Water
-
Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; 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
Chandrasekhar, J.2
Madura, J.D.3
Impey, R.W.4
Klein, M.L.5
-
18
-
-
33745356391
-
Contact Electron-Spin Coupling of Nuclear Magnetic Moments
-
Karplus, M. Contact Electron-Spin Coupling of Nuclear Magnetic Moments J. Chem. Phys. 1959, 30, 11-15
-
(1959)
J. Chem. Phys.
, vol.30
, pp. 11-15
-
-
Karplus, M.1
-
19
-
-
34547670259
-
Limits on Variations in Protein Backbone Dynamics from Precise Measurements of Scalar Couplings
-
Vogeli, B.; Ying, J. F.; Grishaev, A.; Bax, A. Limits on Variations in Protein Backbone Dynamics from Precise Measurements of Scalar Couplings J. Am. Chem. Soc. 2007, 129, 9377-9385
-
(2007)
J. Am. Chem. Soc.
, vol.129
, pp. 9377-9385
-
-
Vogeli, B.1
Ying, J.F.2
Grishaev, A.3
Bax, A.4
-
20
-
-
0030764469
-
Determination of Phi and Chi(1) Angles in Proteins from 13C-13C Three-Bond J Couplings Measured by Three-Dimensional Heteronuclear NMR. How Planar Is the Peptide Bond?
-
Hu, J. S.; Bax, A. Determination of Phi and Chi(1) Angles in Proteins from 13C-13C Three-Bond J Couplings Measured by Three-Dimensional Heteronuclear NMR. How Planar Is the Peptide Bond? J. Am. Chem. Soc. 1997, 119, 6360-6368
-
(1997)
J. Am. Chem. Soc.
, vol.119
, pp. 6360-6368
-
-
Hu, J.S.1
Bax, A.2
-
21
-
-
84857463877
-
Systematic Validation of Protein Force Fields against Experimental Data
-
Lindorff-Larsen, K.; Maragakis, P.; Piana, S.; Eastwood, M. P.; Dror, R. O.; Shaw, D. E. Systematic Validation of Protein Force Fields against Experimental Data PLoS One 2012, 7, e32131
-
(2012)
PLoS One
, vol.7
, pp. 32131
-
-
Lindorff-Larsen, K.1
Maragakis, P.2
Piana, S.3
Eastwood, M.P.4
Dror, R.O.5
Shaw, D.E.6
-
22
-
-
84903486909
-
Residue-Specific Force Field Based on the Protein Coil Library. RSFF1: Modification of OPLS-AA/L
-
Jiang, F.; Zhou, C. Y.; Wu, Y. D. Residue-Specific Force Field Based on the Protein Coil Library. RSFF1: Modification of OPLS-AA/L J. Phys. Chem. B 2014, 118, 6983-6998
-
(2014)
J. Phys. Chem. B
, vol.118
, pp. 6983-6998
-
-
Jiang, F.1
Zhou, C.Y.2
Wu, Y.D.3
-
23
-
-
84901675920
-
Are Current Atomistic Force Fields Accurate Enough to Study Proteins in Crowded Environments?
-
Petrov, D.; Zagrovic, B. Are Current Atomistic Force Fields Accurate Enough to Study Proteins in Crowded Environments? PLoS Comput. Biol. 2014, 10, e1003638
-
(2014)
PLoS Comput. Biol.
, vol.10
, pp. 1003638
-
-
Petrov, D.1
Zagrovic, B.2
-
24
-
-
46249092554
-
GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation
-
Hess, B.; Kutzner, C.; van der Spoel, D.; Lindahl, E. GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation J. Chem. Theory Comput. 2008, 4, 435-447
-
(2008)
J. Chem. Theory Comput.
, vol.4
, pp. 435-447
-
-
Hess, B.1
Kutzner, C.2
Van Der Spoel, D.3
Lindahl, E.4
-
25
-
-
27344454932
-
GROMACS: Fast, Flexible, and Free
-
Van der Spoel, D.; Lindahl, E.; Hess, B.; Groenhof, G.; Mark, A. E.; Berendsen, H. J. C. GROMACS: Fast, Flexible, and Free J. Comput. Chem. 2005, 26, 1701-1718
-
(2005)
J. Comput. Chem.
, vol.26
, pp. 1701-1718
-
-
Van Der Spoel, D.1
Lindahl, E.2
Hess, B.3
Groenhof, G.4
Mark, A.E.5
Berendsen, H.J.C.6
-
26
-
-
0033579417
-
NMR Structure of an F-Actin-Binding Headpiece Motif from Villin
-
Vardar, D.; Buckley, D. A.; Frank, B. S.; McKnight, C. J. NMR Structure of an F-Actin-Binding Headpiece Motif from Villin J. Mol. Biol. 1999, 294, 1299-1310
-
(1999)
J. Mol. Biol.
, vol.294
, pp. 1299-1310
-
-
Vardar, D.1
Buckley, D.A.2
Frank, B.S.3
Mcknight, C.J.4
-
27
-
-
0029879363
-
Determination of the Backbone Dihedral Angles Phi in Human Ubiquitin from Reparametrized Empirical Karplus Equations
-
Wang, A. C.; Bax, A. Determination of the Backbone Dihedral Angles Phi in Human Ubiquitin from Reparametrized Empirical Karplus Equations J. Am. Chem. Soc. 1996, 118, 2483-2494
-
(1996)
J. Am. Chem. Soc.
, vol.118
, pp. 2483-2494
-
-
Wang, A.C.1
Bax, A.2
-
28
-
-
0033082341
-
Solution Structure of a Lipid Transfer Protein Extracted from Rice Seeds - Comparison with Homologous Proteins
-
Poznanski, J.; Sodano, P.; Suh, S. W.; Lee, J. Y.; Ptak, M.; Vovelle, F. Solution Structure of a Lipid Transfer Protein Extracted from Rice Seeds - Comparison with Homologous Proteins Eur. J. Biochem. 1999, 259, 692-708
-
(1999)
Eur. J. Biochem.
, vol.259
, pp. 692-708
-
-
Poznanski, J.1
Sodano, P.2
Suh, S.W.3
Lee, J.Y.4
Ptak, M.5
Vovelle, F.6
-
29
-
-
0034742692
-
Assignment of the 1H, 13C and 15N Resonances of the PPIase Domain of the Trigger Factor from Mycoplasma Genitalium
-
Parac, T. N.; Vogtherr, M.; Maurer, M.; Pahl, A.; Ruterjans, H.; Griesinger, C.; Fiebig, K. Assignment of the 1H, 13C and 15N Resonances of the PPIase Domain of the Trigger Factor from Mycoplasma Genitalium J. Biomol. NMR 2001, 20, 193-194
-
(2001)
J. Biomol. NMR
, vol.20
, pp. 193-194
-
-
Parac, T.N.1
Vogtherr, M.2
Maurer, M.3
Pahl, A.4
Ruterjans, H.5
Griesinger, C.6
Fiebig, K.7
-
30
-
-
12044259775
-
Quantitative J Correlation - A New Approach for Measuring Homonuclear 3-Bond J(H(N)H(Alpha) Coupling-Constants in 15N-Enriched Proteins
-
Vuister, G. W.; Bax, A. Quantitative J Correlation - A New Approach for Measuring Homonuclear 3-Bond J(H(N)H(Alpha) Coupling-Constants in 15N-Enriched Proteins J. Am. Chem. Soc. 1993, 115, 7772-7777
-
(1993)
J. Am. Chem. Soc.
, vol.115
, pp. 7772-7777
-
-
Vuister, G.W.1
Bax, A.2
-
31
-
-
33645961739
-
A Smooth Particle Mesh Ewald Method
-
Essmann, U.; Perera, L.; Berkowitz, M. L.; Darden, T.; Lee, H.; Pedersen, L. G. 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.G.6
-
32
-
-
0000388705
-
LINCS: A Linear Constraint Solver for Molecular Simulations
-
Hess, B.; Bekker, H.; Berendsen, H. J. C.; Fraaije, J. G. E. M. LINCS: A Linear Constraint Solver for Molecular Simulations J. Comput. Chem. 1997, 18, 1463-1472
-
(1997)
J. Comput. Chem.
, vol.18
, pp. 1463-1472
-
-
Hess, B.1
Bekker, H.2
Berendsen, H.J.C.3
Fraaije, J.G.E.M.4
|