-
3
-
-
41149156394
-
α chemical shifts to determine, refine, and validate protein structures
-
in press
-
α chemical shifts to determine, refine, and validate protein structures. Proteins, in press.
-
(2007)
Proteins
-
-
Vila, J.A.1
Scheraga, H.A.2
-
4
-
-
0036129107
-
Probability-based protein secondary structure identification using combined NMR chemical-shift data
-
Wang Y, Jardetzky O (2002) Probability-based protein secondary structure identification using combined NMR chemical-shift data. Protein Sci 11:852-861.
-
(2002)
Protein Sci
, vol.11
, pp. 852-861
-
-
Wang, Y.1
Jardetzky, O.2
-
5
-
-
0035544152
-
13C′ chemical shifts in proteins using a density functional database
-
13C′ chemical shifts in proteins using a density functional database. J Biomol NMR 21:321-333.
-
(2001)
J Biomol NMR
, vol.21
, pp. 321-333
-
-
Xu, X.-P.1
Case, D.A.2
-
6
-
-
1842611349
-
Factors involved in the stability of isolated β-sheets: Turn sequence, β-sheet twisting, and hydrophobic surface burial
-
Santiveri CM, Santoro J, Rico M, Jiménez MA (2004) Factors involved in the stability of isolated β-sheets: Turn sequence, β-sheet twisting, and hydrophobic surface burial. Protein Sci 13:1134-1147.
-
(2004)
Protein Sci
, vol.13
, pp. 1134-1147
-
-
Santiveri, C.M.1
Santoro, J.2
Rico, M.3
Jiménez, M.A.4
-
7
-
-
31944443456
-
Free energy surfaces of miniproteins with a ββα motif: Replica exchange molecular dynamics simulation with an implicit solvation model
-
Jang S, Kim E, Pak Y (2006) Free energy surfaces of miniproteins with a ββα motif: Replica exchange molecular dynamics simulation with an implicit solvation model. Proteins 62:663-671.
-
(2006)
Proteins
, vol.62
, pp. 663-671
-
-
Jang, S.1
Kim, E.2
Pak, Y.3
-
8
-
-
0141704162
-
Free energy landscape of protein folding in water: Explicit vs. implicit solvent
-
Zhou R (2003) Free energy landscape of protein folding in water: Explicit vs. implicit solvent. Proteins 53:148-161.
-
(2003)
Proteins
, vol.53
, pp. 148-161
-
-
Zhou, R.1
-
9
-
-
33751242479
-
Folding of proteins with diverse folds
-
Mohanty S, Hansmann UHE (2006) Folding of proteins with diverse folds. Biophys J 91:3573-3578.
-
(2006)
Biophys J
, vol.91
, pp. 3573-3578
-
-
Mohanty, S.1
Hansmann, U.H.E.2
-
10
-
-
34447511613
-
Parallel tempering molecular dynamics folding simulation of a signal peptide in explicit water
-
Höfinger S, Almeida B, Hansmann UHE (2007) Parallel tempering molecular dynamics folding simulation of a signal peptide in explicit water. Proteins 68:662-669.
-
(2007)
Proteins
, vol.68
, pp. 662-669
-
-
Höfinger, S.1
Almeida, B.2
Hansmann, U.H.E.3
-
12
-
-
0028988451
-
1H-NMR chemical-shifts to measure the quality of protein structures
-
1H-NMR chemical-shifts to measure the quality of protein structures. J Mol Biol 247:541-546.
-
(1995)
J Mol Biol
, vol.247
, pp. 541-546
-
-
Williamson, M.P.1
Kikuchi, J.2
Asajura, T.3
-
13
-
-
0031202856
-
Model-free approach beyond the borders of its applicability
-
Korzhnev DM, Orekhov VY, Arseniev AS (1997) Model-free approach beyond the borders of its applicability. J Magn Reson 127:184-191.
-
(1997)
J Magn Reson
, vol.127
, pp. 184-191
-
-
Korzhnev, D.M.1
Orekhov, V.Y.2
Arseniev, A.S.3
-
14
-
-
4243155782
-
NMR characterization of the dynamics of biomacromolecules
-
Palmer AG, III (2004) NMR characterization of the dynamics of biomacromolecules. Chem Rev 104:3623-3640.
-
(2004)
Chem Rev
, vol.104
, pp. 3623-3640
-
-
Palmer III, A.G.1
-
15
-
-
27544456339
-
A simple method to predict protein flexibility using secondary chemical shifts
-
Berjanskii M, Wishart DS (2005) A simple method to predict protein flexibility using secondary chemical shifts. J Am Chem Soc 127:14970-14971.
-
(2005)
J Am Chem Soc
, vol.127
, pp. 14970-14971
-
-
Berjanskii, M.1
Wishart, D.S.2
-
16
-
-
34547563370
-
The RCI server: Rapid and accurate calculation of protein flexibility using chemical shifts
-
Berjanskii M, Wishart DS (2007) The RCI server: Rapid and accurate calculation of protein flexibility using chemical shifts. Nucleic Acids Res 35:W531-W537.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Berjanskii, M.1
Wishart, D.S.2
-
17
-
-
0001415022
-
-
Cambridge Univ Press, Cambridge, UK, 2nd Ed, pp
-
Press HW, Teukolsky SA, Vetterling WT, Flannery BP (1992) Numerical Recipes in FORTRAN 77: The Art of Scientific Computing (Cambridge Univ Press, Cambridge, UK), 2nd Ed, pp 630-633.
-
(1992)
Numerical Recipes in FORTRAN 77: The Art of Scientific Computing
, pp. 630-633
-
-
Press, H.W.1
Teukolsky, S.A.2
Vetterling, W.T.3
Flannery, B.P.4
-
18
-
-
0001731773
-
Energy parameters in polypeptides. 10. Improved geometrical parameters and nonbonded interactions for use in the ECEPP/3 algorithm, with application to proline-containing peptides
-
Némethy G, et al. (1992) Energy parameters in polypeptides. 10. Improved geometrical parameters and nonbonded interactions for use in the ECEPP/3 algorithm, with application to proline-containing peptides. J Phys Chem 96:6472-6484.
-
(1992)
J Phys Chem
, vol.96
, pp. 6472-6484
-
-
Némethy, G.1
-
19
-
-
0025398721
-
WHAT IF - A molecular modeling and drug design program
-
Vriend GJ (1990) WHAT IF - A molecular modeling and drug design program. J Mol Graphics 8:52-56.
-
(1990)
J Mol Graphics
, vol.8
, pp. 52-56
-
-
Vriend, G.J.1
-
20
-
-
0026259488
-
Improved efficiency of protein structure calculations from NMR data using the program DIANA with redundant dihedral angle constraints
-
Güntert P, Wüthrich K (1991) Improved efficiency of protein structure calculations from NMR data using the program DIANA with redundant dihedral angle constraints. J Biomol NMR 1:447-456.
-
(1991)
J Biomol NMR
, vol.1
, pp. 447-456
-
-
Güntert, P.1
Wüthrich, K.2
-
21
-
-
0004579606
-
13C NMR of protected tetrapeptides TFA-Gly-Gly-L-X-L-Ala-OCH3, where X stands for 20 common amino-acids
-
13C NMR of protected tetrapeptides TFA-Gly-Gly-L-X-L-Ala-OCH3, where X stands for 20 common amino-acids. J Magn Reson 13:217-225.
-
(1974)
J Magn Reson
, vol.13
, pp. 217-225
-
-
Grathwohl, C.1
Wüthrich, K.2
-
22
-
-
0347610773
-
13C nuclear magnetic resonance chemical shifts
-
13C nuclear magnetic resonance chemical shifts. J Am Chem Soc 113:5490-5492.
-
(1991)
J Am Chem Soc
, vol.113
, pp. 5490-5492
-
-
Spera, S.1
Bax, A.2
-
23
-
-
37848999781
-
Application of the random coil index to studying protein flexibility
-
Berjanskii M, Wishart DS (2007) Application of the random coil index to studying protein flexibility. J Biomol NMR 40:31-48.
-
(2007)
J Biomol NMR
, vol.40
, pp. 31-48
-
-
Berjanskii, M.1
Wishart, D.S.2
-
24
-
-
0029181728
-
15N random coil NMR chemical-shifts of the common amino-acids. I. Investigations of nearest-neighbor effects
-
15N random coil NMR chemical-shifts of the common amino-acids. I. Investigations of nearest-neighbor effects. J Biomol NMR 5:67-81.
-
(1995)
J Biomol NMR
, vol.5
, pp. 67-81
-
-
Wishart, D.S.1
-
25
-
-
84985733652
-
1H-NMR parameters of the common amino-acid residues measured in aqueous-solutions of the linear tetrapeptides H-Gly-Gly-X-L-Ala-OH
-
Bundi A, Wüthrich K (1979) 1H-NMR parameters of the common amino-acid residues measured in aqueous-solutions of the linear tetrapeptides H-Gly-Gly-X-L-Ala-OH. Biopolymers 18:285-297.
-
(1979)
Biopolymers
, vol.18
, pp. 285-297
-
-
Bundi, A.1
Wüthrich, K.2
-
26
-
-
0036874286
-
Unblocked statistical-coil tetrapeptides and pentapeptides in aqueous solution: A theoretical study
-
Vila JA, Ripoll DR, Baldoni HA, Scheraga HA (2002) Unblocked statistical-coil tetrapeptides and pentapeptides in aqueous solution: A theoretical study. J Biomol NMR 24:245-262.
-
(2002)
J Biomol NMR
, vol.24
, pp. 245-262
-
-
Vila, J.A.1
Ripoll, D.R.2
Baldoni, H.A.3
Scheraga, H.A.4
-
28
-
-
0033613906
-
Native proteins are surface-molten solids: Application of the Lindemann criterion for the solid versus liquid state
-
Zhou Y, Vitkup D, Karplus M (1999) Native proteins are surface-molten solids: Application of the Lindemann criterion for the solid versus liquid state. J Mol Biol 285:1371-1375.
-
(1999)
J Mol Biol
, vol.285
, pp. 1371-1375
-
-
Zhou, Y.1
Vitkup, D.2
Karplus, M.3
-
29
-
-
12744263121
-
Simultaneous determination of protein structure and dynamics
-
Lindorff-Larsen K, et al. (2005) Simultaneous determination of protein structure and dynamics. Nature 433:128-132.
-
(2005)
Nature
, vol.433
, pp. 128-132
-
-
Lindorff-Larsen, K.1
-
30
-
-
0029608647
-
Structural and dynamic properties of a β-hairpin-forming linear peptide. 1. Modeling using ensemble-averaged constraints
-
Constantine KL, et al. (1995) Structural and dynamic properties of a β-hairpin-forming linear peptide. 1. Modeling using ensemble-averaged constraints. J Am Chem Soc 117:10841-10854.
-
(1995)
J Am Chem Soc
, vol.117
, pp. 10841-10854
-
-
Constantine, K.L.1
-
31
-
-
0028232369
-
An assessment of the precision and accuracy of protein structures determined by NMR-Dependence on distance errors
-
Zhao D, Jardetzky O (1994) An assessment of the precision and accuracy of protein structures determined by NMR-Dependence on distance errors. J Mol Biol 239:601-607.
-
(1994)
J Mol Biol
, vol.239
, pp. 601-607
-
-
Zhao, D.1
Jardetzky, O.2
-
32
-
-
0023914645
-
Variable-target-function and buildup procedures for the calculation of protein conformation - Application to bovine pancreatic trypsininhibitor using limited simulated nuclear magnetic resonance data
-
Vásquez M, Scheraga HA (1988) Variable-target-function and buildup procedures for the calculation of protein conformation - Application to bovine pancreatic trypsininhibitor using limited simulated nuclear magnetic resonance data. J Biomol Struct Dyn 5:757-784.
-
(1988)
J Biomol Struct Dyn
, vol.5
, pp. 757-784
-
-
Vásquez, M.1
Scheraga, H.A.2
-
33
-
-
70350674995
-
On the shortest spanning subtree of a graph and the traveling salesman problem
-
Kruskal JB, Jr (1956) On the shortest spanning subtree of a graph and the traveling salesman problem. Proc Am Math Soc 7:48-50.
-
(1956)
Proc Am Math Soc
, vol.7
, pp. 48-50
-
-
Kruskal Jr, J.B.1
-
34
-
-
84988097454
-
Locally dense basis-sets for chemical-shift calculations
-
Chesnut DB, Moore KD (1989) Locally dense basis-sets for chemical-shift calculations. J Comput Chem 10:648-659.
-
(1989)
J Comput Chem
, vol.10
, pp. 648-659
-
-
Chesnut, D.B.1
Moore, K.D.2
-
35
-
-
41149152265
-
-
Frisch MJ, et al. (1998) Gaussian 98 (Gaussian, Pittsburgh), Revision A.7.
-
Frisch MJ, et al. (1998) Gaussian 98 (Gaussian, Pittsburgh), Revision A.7.
-
-
-
-
36
-
-
0029364052
-
15N chemical-shift referencing in biomolecular NMR
-
15N chemical-shift referencing in biomolecular NMR. J Biomol NMR 6:135-140.
-
(1995)
J Biomol NMR
, vol.6
, pp. 135-140
-
-
Wishart, D.S.1
-
37
-
-
0023430366
-
Monte-Carlo-minimization approach to the multiple-minima problem in protein folding
-
Li Z, Scheraga HA (1987) Monte-Carlo-minimization approach to the multiple-minima problem in protein folding. Proc Natl Acad Sci USA 84:6611-6615.
-
(1987)
Proc Natl Acad Sci USA
, vol.84
, pp. 6611-6615
-
-
Li, Z.1
Scheraga, H.A.2
-
38
-
-
0023338543
-
Accessible surface-areas as a measure of the thermodynamic parameters of hydration of peptides
-
Ooi T, Oobatake M, Nemethy G, Scheraga HA (1987) Accessible surface-areas as a measure of the thermodynamic parameters of hydration of peptides. Proc Natl Acad Sci USA 84:3086-3090.
-
(1987)
Proc Natl Acad Sci USA
, vol.84
, pp. 3086-3090
-
-
Ooi, T.1
Oobatake, M.2
Nemethy, G.3
Scheraga, H.A.4
-
39
-
-
0026848752
-
Refinement of the thrombin-bound structure of a hirudin peptide by a restrained electrostatically driven Monte Carlo method
-
Ripoll DR, Ni F (1992) Refinement of the thrombin-bound structure of a hirudin peptide by a restrained electrostatically driven Monte Carlo method. Biopolymers 32:359-365.
-
(1992)
Biopolymers
, vol.32
, pp. 359-365
-
-
Ripoll, D.R.1
Ni, F.2
-
40
-
-
41149130679
-
-
Case DA, et al. (2004) AMBER 8 (Univ of California, San Francisco).
-
Case DA, et al. (2004) AMBER 8 (Univ of California, San Francisco).
-
-
-
|