-
1
-
-
0036725277
-
Molecular dynamics simulations of biomolecules
-
Karplus, M.; McCammon, J. A. Molecular dynamics simulations of biomolecules Nat. Struct. Mol. Biol. 2002, 9, 646-652
-
(2002)
Nat. Struct. Mol. Biol.
, vol.9
, pp. 646-652
-
-
Karplus, M.1
McCammon, J.A.2
-
2
-
-
77955135754
-
Scrutinizing Molecular Mechanics Force Fields on the Submicrosecond Timescale with NMR Data
-
Lange, O. F.; van der Spoel, D.; de Groot, B. L. Scrutinizing Molecular Mechanics Force Fields on the Submicrosecond Timescale with NMR Data. Biophys. J. 99, 647-655;.
-
Biophys. J.
, vol.99
, pp. 647-655
-
-
Lange, O.F.1
Van Der Spoel, D.2
De Groot, B.L.3
-
3
-
-
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, L07-L09
-
(2008)
Biophys. J.
, vol.95
, pp. 07-L09
-
-
Best, R.B.1
Buchete, N.-V.2
Hummer, G.3
-
4
-
-
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
-
5
-
-
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
-
6
-
-
61349154358
-
Correction
-
Best, R. B. Correction Biophys. J. 2008, 95, 4494
-
(2008)
Biophys. J.
, vol.95
, pp. 4494
-
-
Best, R.B.1
-
7
-
-
68949086461
-
Evaluating the Performance of the ff99SB Force Field Based on NMR Scalar Coupling Data
-
Wickstrom, L.; Okur, A.; Simmerling, C. Evaluating the Performance of the ff99SB Force Field Based on NMR Scalar Coupling Data Biophys. J. 2009, 97, 853-856
-
(2009)
Biophys. J.
, vol.97
, pp. 853-856
-
-
Wickstrom, L.1
Okur, A.2
Simmerling, C.3
-
8
-
-
74949106813
-
Intrinsic Propensities of Amino Acid Residues in GxG Peptides Inferred from Amide I′ Band Profiles and NMR Scalar Coupling Constants
-
Hagarman, A.; Measey, T. J.; Mathieu, D.; Schwalbe, H.; Schweitzer-Stenner, R. Intrinsic Propensities of Amino Acid Residues in GxG Peptides Inferred from Amide I′ Band Profiles and NMR Scalar Coupling Constants J. Am. Chem. Soc. 2009, 132, 540-551
-
(2009)
J. Am. Chem. Soc.
, vol.132
, pp. 540-551
-
-
Hagarman, A.1
Measey, T.J.2
Mathieu, D.3
Schwalbe, H.4
Schweitzer-Stenner, R.5
-
9
-
-
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
-
10
-
-
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: Struct., Funct., Bioinf. 2006, 65, 712-725
-
(2006)
Proteins: Struct., Funct., Bioinf.
, vol.65
, pp. 712-725
-
-
Hornak, V.1
Abel, R.2
Okur, A.3
Strockbine, B.4
Roitberg, A.5
Simmerling, C.6
-
11
-
-
77956606590
-
NMR-Based Protein Potentials
-
Li, D.-W.; Brüschweiler, 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
Brüschweiler, R.2
-
12
-
-
79959272960
-
Iterative Optimization of Molecular Mechanics Force Fields from NMR Data of Full-Length Proteins
-
Li, D.-W.; Brüschweiler, R. Iterative Optimization of Molecular Mechanics Force Fields from NMR Data of Full-Length Proteins J. Chem. Theory Comput. 2011, 7, 1773-1782
-
(2011)
J. Chem. Theory Comput.
, vol.7
, pp. 1773-1782
-
-
Li, D.-W.1
Brüschweiler, R.2
-
13
-
-
84876210074
-
PH-Independence of Trialanine and the Effects of Termini Blocking in Short Peptides: A Combined Vibrational, NMR, UVCD, and Molecular Dynamics Study
-
Toal, S.; Meral, D.; Verbaro, D.; Urbanc, B.; Schweitzer-Stenner, R. pH-Independence of Trialanine and the Effects of Termini Blocking in Short Peptides: A Combined Vibrational, NMR, UVCD, and Molecular Dynamics Study J. Phys. Chem. B 2013, 117, 3689-3706
-
(2013)
J. Phys. Chem. B
, vol.117
, pp. 3689-3706
-
-
Toal, S.1
Meral, D.2
Verbaro, D.3
Urbanc, B.4
Schweitzer-Stenner, R.5
-
14
-
-
84907185247
-
Peptide Conformation Analysis Using an Integrated Bayesian Approach
-
Xiao, X.; Kallenbach, N.; Zhang, Y. Peptide Conformation Analysis Using an Integrated Bayesian Approach J. Chem. Theory Comput. 2014, 10, 4152-4159
-
(2014)
J. Chem. Theory Comput.
, vol.10
, pp. 4152-4159
-
-
Xiao, X.1
Kallenbach, N.2
Zhang, Y.3
-
15
-
-
79953744391
-
Discrepancies between Conformational Distributions of a Polyalanine Peptide in Solution Obtained from Molecular Dynamics Force Fields and Amide I′ Band Profiles
-
Verbaro, D.; Ghosh, I.; Nau, W. M.; Schweitzer-Stenner, R. Discrepancies between Conformational Distributions of a Polyalanine Peptide in Solution Obtained from Molecular Dynamics Force Fields and Amide I′ Band Profiles J. Phys. Chem. B 2010, 114, 17201-17208
-
(2010)
J. Phys. Chem. B
, vol.114
, pp. 17201-17208
-
-
Verbaro, D.1
Ghosh, I.2
Nau, W.M.3
Schweitzer-Stenner, R.4
-
16
-
-
82655179918
-
Conformational propensities and residual structures in unfolded peptides and proteins
-
Schweitzer-Stenner, R. Conformational propensities and residual structures in unfolded peptides and proteins Mol. BioSyst. 2012, 8, 122-133
-
(2012)
Mol. BioSyst.
, vol.8
, pp. 122-133
-
-
Schweitzer-Stenner, R.1
-
17
-
-
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
-
18
-
-
84863091846
-
Conformational distributions of denatured and unstructured proteins are similar to those of 20 × 20 blocked dipeptides
-
Oh, K.-I.; Jung, Y.-S.; Hwang, G.-S.; Cho, M. Conformational distributions of denatured and unstructured proteins are similar to those of 20 × 20 blocked dipeptides J. Biomol. NMR 2012, 53, 25-41
-
(2012)
J. Biomol. NMR
, vol.53
, pp. 25-41
-
-
Oh, K.-I.1
Jung, Y.-S.2
Hwang, G.-S.3
Cho, M.4
-
19
-
-
84909606533
-
COFFDROP: A Coarse-Grained Nonbonded Force Field for Proteins Derived from All-Atom Explicit-Solvent Molecular Dynamics Simulations of Amino Acids
-
Andrews, C. T.; Elcock, A. H. COFFDROP: A Coarse-Grained Nonbonded Force Field for Proteins Derived from All-Atom Explicit-Solvent Molecular Dynamics Simulations of Amino Acids J. Chem. Theory Comput. 2014, 10, 5178-5194
-
(2014)
J. Chem. Theory Comput.
, vol.10
, pp. 5178-5194
-
-
Andrews, C.T.1
Elcock, A.H.2
-
20
-
-
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: Struct., Funct., Bioinf. 2010, 78, 1950-1958
-
(2010)
Proteins: Struct., Funct., Bioinf.
, 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
-
21
-
-
2942622288
-
Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew
-
Horn, H. W.; Swope, W. C.; Pitera, J. W.; Madura, J. D.; Dick, T. J.; Hura, G. L.; Head-Gordon, T. Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew J. Chem. Phys. 2004, 120, 9665-9678
-
(2004)
J. Chem. Phys.
, vol.120
, pp. 9665-9678
-
-
Horn, H.W.1
Swope, W.C.2
Pitera, J.W.3
Madura, J.D.4
Dick, T.J.5
Hura, G.L.6
Head-Gordon, T.7
-
22
-
-
0030764469
-
Determination of ρ and χ1 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 ρ and χ1 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
-
23
-
-
77956478902
-
SPARTA+: A modest improvement in empirical NMR chemical shift prediction by means of an artificial neural network
-
Shen, Y.; Bax, A. SPARTA+: a modest improvement in empirical NMR chemical shift prediction by means of an artificial neural network J. Biomol. NMR 2010, 48, 13-22
-
(2010)
J. Biomol. NMR
, vol.48
, pp. 13-22
-
-
Shen, Y.1
Bax, A.2
-
24
-
-
79952141708
-
Populations of the three major backbone conformations in 19 amino acid dipeptides
-
Grdadolnik, J.; Mohacek-Grosev, V.; Baldwin, R. L.; Avbelj, F. Populations of the three major backbone conformations in 19 amino acid dipeptides Proc. Natl. Acad. Sci. U.S.A. 2011, 108, 1794-1798
-
(2011)
Proc. Natl. Acad. Sci. U.S.A.
, vol.108
, pp. 1794-1798
-
-
Grdadolnik, J.1
Mohacek-Grosev, V.2
Baldwin, R.L.3
Avbelj, F.4
-
25
-
-
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
-
26
-
-
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
-
27
-
-
0001538909
-
Canonical dynamics: Equilibrium phase-space distributions
-
Hoover, W. G. Canonical dynamics: Equilibrium phase-space distributions Phys. Rev. A 1985, 31, 1695-1697
-
(1985)
Phys. Rev. A
, vol.31
, pp. 1695-1697
-
-
Hoover, W.G.1
-
28
-
-
34547809547
-
A unified formulation of the constant temperature molecular dynamics methods
-
Nosé, 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
-
-
Nosé, S.1
-
29
-
-
0019707626
-
Polymorphic transitions in single crystals: A new molecular dynamics method
-
Parrinello, M.; Rahman, A. Polymorphic transitions in single crystals: A new molecular dynamics method J. Appl. Phys. 1981, 52, 7182-7190
-
(1981)
J. Appl. Phys.
, vol.52
, pp. 7182-7190
-
-
Parrinello, M.1
Rahman, A.2
-
30
-
-
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
-
(1995)
J. Chem. Phys.
, vol.103
, pp. 8577
-
-
Essmann, U.1
Perera, L.2
Berkowitz, M.L.3
Darden, T.4
Lee, H.5
Pedersen, L.G.6
-
31
-
-
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
-
32
-
-
84855822396
-
Assessment of the Intrinsic Conformational Preferences of Dipeptide Amino Acids in Aqueous Solution by Combined Umbrella Sampling/MBAR Statistics. A Comparison with Experimental Results
-
Cruz, V. L.; Ramos, J.; Martinez-Salazar, J. Assessment of the Intrinsic Conformational Preferences of Dipeptide Amino Acids in Aqueous Solution by Combined Umbrella Sampling/MBAR Statistics. A Comparison with Experimental Results J. Phys. Chem. B 2011, 116, 469-475
-
(2011)
J. Phys. Chem. B
, vol.116
, pp. 469-475
-
-
Cruz, V.L.1
Ramos, J.2
Martinez-Salazar, J.3
-
33
-
-
0028566270
-
A revised set of potentials for β-turn formation in proteins
-
Hutchinson, E. G.; Thornton, J. M. A revised set of potentials for β-turn formation in proteins Protein Sci. 1994, 3, 2207-2216
-
(1994)
Protein Sci.
, vol.3
, pp. 2207-2216
-
-
Hutchinson, E.G.1
Thornton, J.M.2
-
34
-
-
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
-
35
-
-
12044259775
-
Quantitative J correlation: A new approach for measuring homonuclear three-bond J(HNH.alpha.) coupling constants in 15N-enriched proteins
-
Vuister, G. W.; Bax, A. Quantitative J correlation: a new approach for measuring homonuclear three-bond J(HNH.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
-
36
-
-
34547670259
-
Limits on Variations in Protein Backbone Dynamics from Precise Measurements of Scalar Couplings
-
Vögeli, B.; Ying, J.; 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
-
-
Vögeli, B.1
Ying, J.2
Grishaev, A.3
Bax, A.4
-
37
-
-
0345517099
-
Self-consistent 3J coupling analysis for the joint calibration of Karplus coefficients and evaluation of torsion angles
-
Schmidt, J.; Blümel, M.; Löhr, F.; Rüterjans, H. Self-consistent 3J coupling analysis for the joint calibration of Karplus coefficients and evaluation of torsion angles J. Biomol. NMR 1999, 14, 1-12
-
(1999)
J. Biomol. NMR
, vol.14
, pp. 1-12
-
-
Schmidt, J.1
Blümel, M.2
Löhr, F.3
Rüterjans, H.4
-
38
-
-
0021764813
-
Calibration of the angular dependence of the amide proton-Cα proton coupling constants, 3JHNα, in a globular protein: Use of 3JHNα for identification of helical secondary structure
-
Pardi, A.; Billeter, M.; Wüthrich, K. Calibration of the angular dependence of the amide proton-Cα proton coupling constants, 3JHNα, in a globular protein: Use of 3JHNα for identification of helical secondary structure J. Mol. Biol. 1984, 180, 741-751
-
(1984)
J. Mol. Biol.
, vol.180
, pp. 741-751
-
-
Pardi, A.1
Billeter, M.2
Wüthrich, K.3
-
39
-
-
0029879363
-
Determination of the Backbone Dihedral Angles ρ in Human Ubiquitin from Reparametrized Empirical Karplus Equations
-
Wang, A. C.; Bax, A. Determination of the Backbone Dihedral Angles ρ 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
-
40
-
-
0034715485
-
Static and Dynamic Effects on Vicinal Scalar J Couplings in Proteins and Peptides: A MD/DFT Analysis
-
Case, D. A.; Scheurer, C.; Brüschweiler, R. Static and Dynamic Effects on Vicinal Scalar J Couplings in Proteins and Peptides: A MD/DFT Analysis J. Am. Chem. Soc. 2000, 122, 10390-10397
-
(2000)
J. Am. Chem. Soc.
, vol.122
, pp. 10390-10397
-
-
Case, D.A.1
Scheurer, C.2
Brüschweiler, R.3
-
41
-
-
69249206505
-
Structural dynamics of protein backbone ρ angles: Extended molecular dynamics simulations versus experimental 3 J scalar couplings
-
Markwick, P. L.; Showalter, S.; Bouvignies, G.; Brüschweiler, R.; Blackledge, M. Structural dynamics of protein backbone ρ angles: extended molecular dynamics simulations versus experimental 3 J scalar couplings J. Biomol. NMR 2009, 45, 17-21
-
(2009)
J. Biomol. NMR
, vol.45
, pp. 17-21
-
-
Markwick, P.L.1
Showalter, S.2
Bouvignies, G.3
Brüschweiler, R.4
Blackledge, M.5
-
42
-
-
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
-
43
-
-
80051673221
-
SHIFTX2: Significantly improved protein chemical shift prediction
-
Han, B.; Liu, Y.; Ginzinger, S.; Wishart, D. SHIFTX2: significantly improved protein chemical shift prediction J. Biomol. NMR 2011, 50, 43-57
-
(2011)
J. Biomol. NMR
, vol.50
, pp. 43-57
-
-
Han, B.1
Liu, Y.2
Ginzinger, S.3
Wishart, D.4
-
44
-
-
70349627256
-
Fast and Accurate Predictions of Protein NMR Chemical Shifts from Interatomic Distances
-
Kohlhoff, K. J.; Robustelli, P.; Cavalli, A.; Salvatella, X.; Vendruscolo, M. Fast and Accurate Predictions of Protein NMR Chemical Shifts from Interatomic Distances J. Am. Chem. Soc. 2009, 131, 13894-13895
-
(2009)
J. Am. Chem. Soc.
, vol.131
, pp. 13894-13895
-
-
Kohlhoff, K.J.1
Robustelli, P.2
Cavalli, A.3
Salvatella, X.4
Vendruscolo, M.5
-
45
-
-
0037114648
-
Probing multiple effects on 15N, 13Cα, 13Cβ, and 13C′ chemical shifts in peptides using density functional theory
-
Xu, X.-P.; Case, D. A. Probing multiple effects on 15N, 13Cα, 13Cβ, and 13C′ chemical shifts in peptides using density functional theory Biopolymers 2002, 65, 408-423
-
(2002)
Biopolymers
, vol.65
, pp. 408-423
-
-
Xu, X.-P.1
Case, D.A.2
-
46
-
-
84868198915
-
PPM: A side-chain and backbone chemical shift predictor for the assessment of protein conformational ensembles
-
Li, D.-W.; Brüschweiler, R. PPM: a side-chain and backbone chemical shift predictor for the assessment of protein conformational ensembles J. Biomol. NMR 2012, 54, 257-265
-
(2012)
J. Biomol. NMR
, vol.54
, pp. 257-265
-
-
Li, D.-W.1
Brüschweiler, R.2
-
47
-
-
31944437630
-
Intrinsic backbone preferences are fully present in blocked amino acids
-
Avbelj, F.; Grdadolnik, S. G.; Grdadolnik, J.; Baldwin, R. L. Intrinsic backbone preferences are fully present in blocked amino acids Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 1272-1277
-
(2006)
Proc. Natl. Acad. Sci. U.S.A.
, vol.103
, pp. 1272-1277
-
-
Avbelj, F.1
Grdadolnik, S.G.2
Grdadolnik, J.3
Baldwin, R.L.4
-
48
-
-
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 2014, 119, 1035-1047
-
(2014)
J. Phys. Chem. B
, vol.119
, pp. 1035-1047
-
-
Zhou, C.-Y.1
Jiang, F.2
Wu, Y.-D.3
-
49
-
-
77954609748
-
Neighbor-Dependent Ramachandran Probability Distributions of Amino Acids Developed from a Hierarchical Dirichlet Process Model
-
Ting, D.; Wang, G.; Shapovalov, M.; Mitra, R.; Jordan, M. I.; Dunbrack, R. L., Jr. Neighbor-Dependent Ramachandran Probability Distributions of Amino Acids Developed from a Hierarchical Dirichlet Process Model PLoS Comput. Biol. 2010, 6, e1000763
-
(2010)
PLoS Comput. Biol.
, vol.6
, pp. 1000763
-
-
Ting, D.1
Wang, G.2
Shapovalov, M.3
Mitra, R.4
Jordan, M.I.5
Dunbrack, R.L.6
-
50
-
-
0033752859
-
Beta- and Gamma-turns in proteins revisited: A new set of amino acid turn-type dependent positional preferences and potentials
-
Guruprasad, K.; Rajkumar, S. Beta- and Gamma-turns in proteins revisited: a new set of amino acid turn-type dependent positional preferences and potentials J. Biosci. 2000, 25, 14
-
(2000)
J. Biosci.
, vol.25
, pp. 14
-
-
Guruprasad, K.1
Rajkumar, S.2
-
51
-
-
38349091489
-
Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method
-
Barducci, A.; Bussi, G.; Parrinello, M. Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method Phys. Rev. Lett. 2008, 100, 020603
-
(2008)
Phys. Rev. Lett.
, vol.100
, pp. 020603
-
-
Barducci, A.1
Bussi, G.2
Parrinello, M.3
-
52
-
-
84872167078
-
Critical Assessment of Current Force Fields. Short Peptide Test Case
-
Vymětal, J.; Vondrášek, J. Critical Assessment of Current Force Fields. Short Peptide Test Case J. Chem. Theory Comput. 2012, 9, 441-451
-
(2012)
J. Chem. Theory Comput.
, vol.9
, pp. 441-451
-
-
Vymětal, J.1
Vondrášek, J.2
-
53
-
-
58149161566
-
A Hamiltonian Replica Exchange Approach and Its Application to the Study of Side-Chain Type and Neighbor Effects on Peptide Backbone Conformations
-
Xu, C.; Wang, J.; Liu, H. A Hamiltonian Replica Exchange Approach and Its Application to the Study of Side-Chain Type and Neighbor Effects on Peptide Backbone Conformations J. Chem. Theory Comput. 2008, 4, 1348-1359
-
(2008)
J. Chem. Theory Comput.
, vol.4
, pp. 1348-1359
-
-
Xu, C.1
Wang, J.2
Liu, H.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
-
-
80052490430
-
Toward a Predictive Understanding of Slow Methyl Group Dynamics in Proteins
-
Long, D.; Li, D.-W.; Korvin, W. F. A.; Griesinger, C.; Brüschweiler, R. Toward a Predictive Understanding of Slow Methyl Group Dynamics in Proteins Biophys. J. 2011, 101, 910-915
-
(2011)
Biophys. J.
, vol.101
, pp. 910-915
-
-
Long, D.1
Li, D.-W.2
Korvin, W.F.A.3
Griesinger, C.4
Brüschweiler, R.5
-
56
-
-
12244297937
-
Vicinal Proton Coupling in Nuclear Magnetic Resonance
-
Karplus, M. Vicinal Proton Coupling in Nuclear Magnetic Resonance J. Am. Chem. Soc. 1963, 85, 2870-2871
-
(1963)
J. Am. Chem. Soc.
, vol.85
, pp. 2870-2871
-
-
Karplus, M.1
-
57
-
-
84885396839
-
Quantum Mechanical Study of Vicinal J Spin-Spin Coupling Constants for the Protein Backbone
-
Wang, B.; He, X.; Merz, K. M. Quantum Mechanical Study of Vicinal J Spin-Spin Coupling Constants for the Protein Backbone J. Chem. Theory Comput. 2013, 9, 4653-4659
-
(2013)
J. Chem. Theory Comput.
, vol.9
, pp. 4653-4659
-
-
Wang, B.1
He, X.2
Merz, K.M.3
-
58
-
-
84924366750
-
Local Order in the Unfolded State: Conformational Biases and Nearest Neighbor Interactions
-
Toal, S.; Schweitzer-Stenner, R. Local Order in the Unfolded State: Conformational Biases and Nearest Neighbor Interactions Biomolecules 2014, 4, 725-773
-
(2014)
Biomolecules
, vol.4
, pp. 725-773
-
-
Toal, S.1
Schweitzer-Stenner, R.2
-
59
-
-
29144433298
-
Polyproline II propensities from GGXGG peptides reveal an anticorrelation with β-sheet scales
-
Shi, Z.; Chen, K.; Liu, Z.; Ng, A.; Bracken, W. C.; Kallenbach, N. R. Polyproline II propensities from GGXGG peptides reveal an anticorrelation with β-sheet scales Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 17964-17968
-
(2005)
Proc. Natl. Acad. Sci. U.S.A.
, vol.102
, pp. 17964-17968
-
-
Shi, Z.1
Chen, K.2
Liu, Z.3
Ng, A.4
Bracken, W.C.5
Kallenbach, N.R.6
-
60
-
-
0041319047
-
Host-guest scale of left-handed polyproline II helix formation
-
Rucker, A. L.; Pager, C. T.; Campbell, M. N.; Qualls, J. E.; Creamer, T. P. Host-guest scale of left-handed polyproline II helix formation Proteins: Struct., Funct., Bioinf. 2003, 53, 68-75
-
(2003)
Proteins: Struct., Funct., Bioinf.
, vol.53
, pp. 68-75
-
-
Rucker, A.L.1
Pager, C.T.2
Campbell, M.N.3
Qualls, J.E.4
Creamer, T.P.5
-
61
-
-
84862835564
-
A Propensity Scale for Type II Polyproline Helices (PPII): Aromatic Amino Acids in Proline-Rich Sequences Strongly Disfavor PPII Due to Proline-Aromatic Interactions
-
Brown, A. M.; Zondlo, N. J. A Propensity Scale for Type II Polyproline Helices (PPII): Aromatic Amino Acids in Proline-Rich Sequences Strongly Disfavor PPII Due to Proline-Aromatic Interactions Biochemistry 2012, 51, 5041-5051
-
(2012)
Biochemistry
, vol.51
, pp. 5041-5051
-
-
Brown, A.M.1
Zondlo, N.J.2
-
62
-
-
0000084729
-
Sequence-Corrected 15N Random Coil Chemical Shifts
-
Braun, D.; Wider, G.; Wuethrich, K. Sequence-Corrected 15N Random Coil Chemical Shifts J. Am. Chem. Soc. 1994, 116, 8466-8469
-
(1994)
J. Am. Chem. Soc.
, vol.116
, pp. 8466-8469
-
-
Braun, D.1
Wider, G.2
Wuethrich, K.3
-
63
-
-
0034836367
-
Sequence-Dependent Correction of Random Coil NMR Chemical Shifts
-
Schwarzinger, S.; Kroon, G. J. A.; Foss, T. R.; Chung, J.; Wright, P. E.; Dyson, H. J. Sequence-Dependent Correction of Random Coil NMR Chemical Shifts J. Am. Chem. Soc. 2001, 123, 2970-2978
-
(2001)
J. Am. Chem. Soc.
, vol.123
, pp. 2970-2978
-
-
Schwarzinger, S.1
Kroon, G.J.A.2
Foss, T.R.3
Chung, J.4
Wright, P.E.5
Dyson, H.J.6
-
64
-
-
80051704532
-
Sequence correction of random coil chemical shifts: Correlation between neighbor correction factors and changes in the Ramachandran distribution
-
Kjaergaard, M.; Poulsen, F. Sequence correction of random coil chemical shifts: correlation between neighbor correction factors and changes in the Ramachandran distribution J. Biomol. NMR 2011, 50, 157-165
-
(2011)
J. Biomol. NMR
, vol.50
, pp. 157-165
-
-
Kjaergaard, M.1
Poulsen, F.2
-
65
-
-
0030726550
-
NMR analysis of main-chain conformational preferences in an unfolded fibronectin-binding protein
-
Penkett, C. J.; Redfield, C.; Dodd, I.; Hubbard, J.; McBay, D. L.; Mossakowska, D. E.; Smith, R. A. G.; Dobson, C. M.; Smith, L. J. NMR analysis of main-chain conformational preferences in an unfolded fibronectin-binding protein J. Mol. Biol. 1997, 274, 152-159
-
(1997)
J. Mol. Biol.
, vol.274
, pp. 152-159
-
-
Penkett, C.J.1
Redfield, C.2
Dodd, I.3
Hubbard, J.4
McBay, D.L.5
Mossakowska, D.E.6
Smith, R.A.G.7
Dobson, C.M.8
Smith, L.J.9
-
66
-
-
22244458915
-
Helix, Sheet, and Polyproline II Frequencies and Strong Nearest Neighbor Effects in a Restricted Coil Library
-
Jha, A. K.; Colubri, A.; Zaman, M. H.; Koide, S.; Sosnick, T. R.; Freed, K. F. Helix, Sheet, and Polyproline II Frequencies and Strong Nearest Neighbor Effects in a Restricted Coil Library Biochemistry 2005, 44, 9691-9702
-
(2005)
Biochemistry
, vol.44
, pp. 9691-9702
-
-
Jha, A.K.1
Colubri, A.2
Zaman, M.H.3
Koide, S.4
Sosnick, T.R.5
Freed, K.F.6
-
67
-
-
33845675698
-
Computational basis of knowledge-based conformational probabilities derived from local- and long-range interactions in proteins
-
Ormeci, L.; Gursoy, A.; Tunca, G.; Erman, B. Computational basis of knowledge-based conformational probabilities derived from local- and long-range interactions in proteins Proteins: Struct., Funct., Bioinf. 2007, 66, 29-40
-
(2007)
Proteins: Struct., Funct., Bioinf.
, vol.66
, pp. 29-40
-
-
Ormeci, L.1
Gursoy, A.2
Tunca, G.3
Erman, B.4
-
68
-
-
4344697167
-
Local Propensities and Statistical Potentials of Backbone Dihedral Angles in Proteins
-
Betancourt, M. R.; Skolnick, J. Local Propensities and Statistical Potentials of Backbone Dihedral Angles in Proteins J. Mol. Biol. 2004, 342, 635-649
-
(2004)
J. Mol. Biol.
, vol.342
, pp. 635-649
-
-
Betancourt, M.R.1
Skolnick, J.2
-
69
-
-
0032545189
-
Modulation of intrinsic ρ,ψ propensities of amino acids by neighbouring residues in the coil regions of protein structures: NMR analysis and dissection of a β-hairpin peptide
-
Griffiths-Jones, S. R.; Sharman, G. J.; Maynard, A. J.; Searle, M. S. Modulation of intrinsic ρ,ψ propensities of amino acids by neighbouring residues in the coil regions of protein structures: NMR analysis and dissection of a β-hairpin peptide J. Mol. Biol. 1998, 284, 1597-1609
-
(1998)
J. Mol. Biol.
, vol.284
, pp. 1597-1609
-
-
Griffiths-Jones, S.R.1
Sharman, G.J.2
Maynard, A.J.3
Searle, M.S.4
-
70
-
-
0033730431
-
The Flory isolated-pair hypothesis is not valid for polypeptide chains: Implications for protein folding
-
Pappu, R. V.; Srinivasan, R.; Rose, G. D. The Flory isolated-pair hypothesis is not valid for polypeptide chains: Implications for protein folding Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 12565-12570
-
(2000)
Proc. Natl. Acad. Sci. U.S.A.
, vol.97
, pp. 12565-12570
-
-
Pappu, R.V.1
Srinivasan, R.2
Rose, G.D.3
-
71
-
-
0042701995
-
Investigations into Sequence and Conformational Dependence of Backbone Entropy, Inter-basin Dynamics and the Flory Isolated-pair Hypothesis for Peptides
-
Zaman, M. H.; Shen, M.-Y.; Berry, R. S.; Freed, K. F.; Sosnick, T. R. Investigations into Sequence and Conformational Dependence of Backbone Entropy, Inter-basin Dynamics and the Flory Isolated-pair Hypothesis for Peptides J. Mol. Biol. 2003, 331, 693-711
-
(2003)
J. Mol. Biol.
, vol.331
, pp. 693-711
-
-
Zaman, M.H.1
Shen, M.-Y.2
Berry, R.S.3
Freed, K.F.4
Sosnick, T.R.5
-
72
-
-
23944453852
-
Reconciling Observations of Sequence-Specific Conformational Propensities with the Generic Polymeric Behavior of Denatured Proteins
-
Tran, H. T.; Wang, X.; Pappu, R. V. Reconciling Observations of Sequence-Specific Conformational Propensities with the Generic Polymeric Behavior of Denatured Proteins† Biochemistry 2005, 44, 11369-11380
-
(2005)
Biochemistry
, vol.44
, pp. 11369-11380
-
-
Tran, H.T.1
Wang, X.2
Pappu, R.V.3
-
73
-
-
4444282928
-
A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6
-
Oostenbrink, C.; Villa, A.; Mark, A. E.; Van Gunsteren, W. F. A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6 J. Comput. Chem. 2004, 25, 1656-1676
-
(2004)
J. Comput. Chem.
, vol.25
, pp. 1656-1676
-
-
Oostenbrink, C.1
Villa, A.2
Mark, A.E.3
Van Gunsteren, W.F.4
-
74
-
-
84857783671
-
A comprehensive library of blocked dipeptides reveals intrinsic backbone conformational propensities of unfolded proteins
-
Oh, K.-I.; Lee, K.-K.; Park, E.-K.; Jung, Y.; Hwang, G.-S.; Cho, M. A comprehensive library of blocked dipeptides reveals intrinsic backbone conformational propensities of unfolded proteins Proteins: Struct., Funct., Bioinf. 2012, 80, 977-990
-
(2012)
Proteins: Struct., Funct., Bioinf.
, vol.80
, pp. 977-990
-
-
Oh, K.-I.1
Lee, K.-K.2
Park, E.-K.3
Jung, Y.4
Hwang, G.-S.5
Cho, M.6
-
75
-
-
0242663237
-
A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations
-
Duan, Y.; Wu, C.; Chowdhury, S.; Lee, M. C.; Xiong, G.; Zhang, W.; Yang, R.; Cieplak, P.; Luo, R.; Lee, T.; Caldwell, J.; Wang, J.; Kollman, P. A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations J. Comput. Chem. 2003, 24, 1999-2012
-
(2003)
J. Comput. Chem.
, vol.24
, pp. 1999-2012
-
-
Duan, Y.1
Wu, C.2
Chowdhury, S.3
Lee, M.C.4
Xiong, G.5
Zhang, W.6
Yang, R.7
Cieplak, P.8
Luo, R.9
Lee, T.10
Caldwell, J.11
Wang, J.12
Kollman, P.13
-
76
-
-
3342969223
-
Origin of the neighboring residue effect on peptide backbone conformation
-
Avbelj, F.; Baldwin, R. L. Origin of the neighboring residue effect on peptide backbone conformation Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 10967-10972
-
(2004)
Proc. Natl. Acad. Sci. U.S.A.
, vol.101
, pp. 10967-10972
-
-
Avbelj, F.1
Baldwin, R.L.2
|