-
1
-
-
0034646573
-
Chemical dissection and reassembly of amyloid fibrils formed by a peptide fragment of transthyretin
-
MacPhee CE, Dobson CM. Chemical dissection and reassembly of amyloid fibrils formed by a peptide fragment of transthyretin. J. Mol. Biol. 2000; 297: 1203-1215.
-
(2000)
J. Mol. Biol.
, vol.297
, pp. 1203-1215
-
-
MacPhee, C.E.1
Dobson, C.M.2
-
2
-
-
0035961329
-
The structural basis of protein folding and its links with human disease
-
Dobson CM. The structural basis of protein folding and its links with human disease. Philos. Trans. R. Soc. Lond. Ser. B-Biol. Sci. 2001; 356: 133-145.
-
(2001)
Philos. Trans. R. Soc. Lond. Ser. B-Biol. Sci.
, vol.356
, pp. 133-145
-
-
Dobson, C.M.1
-
4
-
-
0027391780
-
Capping interactions in isolated α-helices: Position- dependent substitution effects and structure of a serine-capped peptide helix
-
Lyu PC, Wemmer DE, Zhou HX, Pinker RJ, Kallenbach NR. Capping interactions in isolated α-helices: Position- dependent substitution effects and structure of a serine-capped peptide helix. Biochemistry 1993; 32: 421-425.
-
(1993)
Biochemistry
, vol.32
, pp. 421-425
-
-
Lyu, P.C.1
Wemmer, D.E.2
Zhou, H.X.3
Pinker, R.J.4
Kallenbach, N.R.5
-
5
-
-
0027245441
-
A single-stranded amphipathic α-helix in aqueous-solution: Design, structural characterization, and its application for determining α-helical propensities of amino-acids
-
Zhou NE, Kay CM, Sykes BD, Hodges RS. A single-stranded amphipathic α-helix in aqueous-solution: Design, structural characterization, and its application for determining α-helical propensities of amino-acids. Biochemistry 1993; 32: 6190-6197.
-
(1993)
Biochemistry
, vol.32
, pp. 6190-6197
-
-
Zhou, N.E.1
Kay, C.M.2
Sykes, B.D.3
Hodges, R.S.4
-
6
-
-
0029028490
-
α-Helix formation by peptides of defined sequence
-
Baldwin RL. α-Helix formation by peptides of defined sequence. Biophys. Chem 1995; 55: 127-135.
-
(1995)
Biophys. Chem
, vol.55
, pp. 127-135
-
-
Baldwin, R.L.1
-
7
-
-
0031127043
-
Development of the multiple sequence approximation within the AGADIR model of α-helix formation: Comparison with Zimm-Bragg and Lifson-Roig formalisms
-
Muñoz V, Serrano L. Development of the multiple sequence approximation within the AGADIR model of α-helix formation: Comparison with Zimm-Bragg and Lifson-Roig formalisms. Biopolymers 1997; 41: 495-509.
-
(1997)
Biopolymers
, vol.41
, pp. 495-509
-
-
Muñoz, V.1
Serrano, L.2
-
9
-
-
0001117058
-
Construction and design of β-sheets
-
Smith CK, Regan L. Construction and design of β-sheets. Acc. Chem. Res. 1997; 30: 153-161.
-
(1997)
Acc. Chem. Res.
, vol.30
, pp. 153-161
-
-
Smith, C.K.1
Regan, L.2
-
11
-
-
0032246263
-
Minimal model systems for β-sheet secondary structure in proteins
-
Gellman SH. Minimal model systems for β-sheet secondary structure in proteins. Curr. Opin. Chem. Biol. 1998; 2: 717-725.
-
(1998)
Curr. Opin. Chem. Biol.
, vol.2
, pp. 717-725
-
-
Gellman, S.H.1
-
13
-
-
0034581611
-
The relationship between sequence and structure in elementary folding units
-
Serrano L. The relationship between sequence and structure in elementary folding units. Adv. Prot. Chem. 2000; 53: 49-85.
-
(2000)
Adv. Prot. Chem.
, vol.53
, pp. 49-85
-
-
Serrano, L.1
-
15
-
-
0021844602
-
β-Hairpin families in globular-proteins
-
Sibanda BL, Thornton JM. β-Hairpin families in globular-proteins. Nature 1985; 316: 170-174.
-
(1985)
Nature
, vol.316
, pp. 170-174
-
-
Sibanda, B.L.1
Thornton, J.M.2
-
16
-
-
0024391832
-
Conformation of β-hairpins in protein structures. A systematic classification with applications to modeling by homology, electron-density fitting and protein engineering
-
Sibanda BL, Blundell TL, Thornton JM. Conformation of β-hairpins in protein structures. A systematic classification with applications to modeling by homology, electron-density fitting and protein engineering. J. Mol. Biol. 1989; 206: 759-777.
-
(1989)
J. Mol. Biol.
, vol.206
, pp. 759-777
-
-
Sibanda, B.L.1
Blundell, T.L.2
Thornton, J.M.3
-
17
-
-
0026351935
-
Conformation of β-hairpins in protein structures. Classification and diversity in homologous structures
-
Sibanda BL, Thornton JM. Conformation of β-hairpins in protein structures. Classification and diversity in homologous structures. Methods Enzymol, 1991; 202: 59-82.
-
(1991)
Methods Enzymol.
, vol.202
, pp. 59-82
-
-
Sibanda, B.L.1
Thornton, J.M.2
-
19
-
-
0032584783
-
Reversible peptide folding in solution by molecular dynamics simulation
-
Daura X, Jaun B, Seebach D, van Gunsteren WF, Mark AE. Reversible peptide folding in solution by molecular dynamics simulation. J. Mol. Biol. 1998; 280: 925-932.
-
(1998)
J. Mol. Biol.
, vol.280
, pp. 925-932
-
-
Daura, X.1
Jaun, B.2
Seebach, D.3
van Gunsteren, W.F.4
Mark, A.E.5
-
20
-
-
0032561237
-
Pathways to a protein folding intermediate observed in a 1- microsecond simulation in aqueous solution
-
Duan Y, Kollman PA. Pathways to a protein folding intermediate observed in a 1- microsecond simulation in aqueous solution. Science 1998; 282: 740-744.
-
(1998)
Science
, vol.282
, pp. 740-744
-
-
Duan, Y.1
Kollman, P.A.2
-
21
-
-
0032484151
-
Solution conformations and thermodynamics of structured peptides: Molecular dynamics simulation with an implicit solvation model
-
Schäfer M, Bartels C, Karplus M. Solution conformations and thermodynamics of structured peptides: Molecular dynamics simulation with an implicit solvation model. J. Mol. Biol, 1998; 284: 835-848.
-
(1998)
J. Mol. Biol.
, vol.284
, pp. 835-848
-
-
Schäfer, M.1
Bartels, C.2
Karplus, M.3
-
22
-
-
0033518605
-
Molecular dynamics of a 15-residue poly(L-alanine) in water: Helix formation and energetics
-
Takano M, Yamato T, Higo J, Suyama A, Nagayama K. Molecular dynamics of a 15-residue poly(L-alanine) in water: Helix formation and energetics. J. Am. Chem. Soc. 1999; 121: 605-612.
-
(1999)
J. Am. Chem. Soc.
, vol.121
, pp. 605-612
-
-
Takano, M.1
Yamato, T.2
Higo, J.3
Suyama, A.4
Nagayama, K.5
-
23
-
-
0035179018
-
Helix nucleation kinetics from molecular simulations in explicit solvent
-
Hummer G, Garcia AE, Garde S. Helix nucleation kinetics from molecular simulations in explicit solvent. Proteins: Struct. Funct. Genet. 2001; 42: 77-84.
-
(2001)
Proteins: Struct. Funct. Genet.
, vol.42
, pp. 77-84
-
-
Hummer, G.1
Garcia, A.E.2
Garde, S.3
-
24
-
-
0037174385
-
All-atom structure prediction and folding simulations of a stable protein
-
Simmerling C, Strockbine B, Roitberg AE. All-atom structure prediction and folding simulations of a stable protein. J. Am. Chem. Soc. 2002; 124: 11 258-11 259.
-
(2002)
J. Am. Chem. Soc.
, vol.124
-
-
Simmerling, C.1
Strockbine, B.2
Roitberg, A.E.3
-
25
-
-
0037038372
-
Absolute comparison of simulated and experimental protein-folding dynamics
-
Snow CD, Nguyen H, Pande VS, Gruebele M. Absolute comparison of simulated and experimental protein-folding dynamics. Nature 2002; 420: 102-106.
-
(2002)
Nature
, vol.420
, pp. 102-106
-
-
Snow, C.D.1
Nguyen, H.2
Pande, V.S.3
Gruebele, M.4
-
26
-
-
1842334454
-
Refolding simulations of an isolated fragment of barnase into a native-like β-hairpin: Evidence for compactness and hydrogen bonding as concurrent stabilizing factors
-
Prévost M, Ortmans I. Refolding simulations of an isolated fragment of barnase into a native-like β-hairpin: Evidence for compactness and hydrogen bonding as concurrent stabilizing factors. Proteins: Struct. Funct. Genet. 1997; 29: 212-227.
-
(1997)
Proteins: Struct. Funct. Genet.
, vol.29
, pp. 212-227
-
-
Prévost, M.1
Ortmans, I.2
-
28
-
-
0033529908
-
Molecular dynamics simulations of unfolding and refolding of β-hairpin fragment of protein G
-
Pande VS, Rokhsar DS. Molecular dynamics simulations of unfolding and refolding of β-hairpin fragment of protein G. Proc. Natl Acad. Sci. USA 1999; 96: 9062-9067.
-
(1999)
Proc. Natl. Acad. Sci. USA
, vol.96
, pp. 9062-9067
-
-
Pande, V.S.1
Rokhsar, D.S.2
-
29
-
-
0032881707
-
A molecular dynamics study of the 41-56 β-hairpin from B1 domain of protein G
-
Roccatano D, Amadei A, Di Nola A, Berendsen HJ. A molecular dynamics study of the 41-56 β-hairpin from B1 domain of protein G. Protein Sci. 1999; 8: 2130-2143.
-
(1999)
Protein Sci.
, vol.8
, pp. 2130-2143
-
-
Roccatano, D.1
Amadei, A.2
Di Nola, A.3
Berendsen, H.J.4
-
30
-
-
0034635340
-
β-Hairpin stability and folding: Molecular dynamics studies of the first β-hairpin of tendamistat
-
Bonvin AMJJ, van Gunsteren WF. β-Hairpin stability and folding: Molecular dynamics studies of the first β-hairpin of tendamistat. J. Mol. Biol. 2000; 296: 255-268.
-
(2000)
J. Mol. Biol.
, vol.296
, pp. 255-268
-
-
Bonvin, A.M.J.J.1
van Gunsteren, W.F.2
-
31
-
-
0034718553
-
Folding simulations of a three-stranded antiparallel β-sheet peptide
-
Ferrara P, Caflisch A. Folding simulations of a three-stranded antiparallel β-sheet peptide. Proc. Natl Acad. Sci, USA 2000; 97: 10 780-10 785.
-
(2000)
Proc. Natl. Acad. Sci. USA
, vol.97
-
-
Ferrara, P.1
Caflisch, A.2
-
32
-
-
0034598946
-
Molecular dynamics simulations of a β-hairpin fragment of protein G: Balance between side-chain and backbone forces
-
Ma BY, Nussinov R. Molecular dynamics simulations of a β-hairpin fragment of protein G: Balance between side-chain and backbone forces. J. Mol. Biol. 2000; 296: 1091-1104.
-
(2000)
J. Mol. Biol.
, vol.296
, pp. 1091-1104
-
-
Ma, B.Y.1
Nussinov, R.2
-
33
-
-
0034620730
-
Molecular dynamics simulations of three-strand β-sheet folding
-
Wang HW, Sung SS. Molecular dynamics simulations of three-strand β-sheet folding. J. Am. Chem. Soc. 2000; 122: 1999-2009.
-
(2000)
J. Am. Chem. Soc.
, vol.122
, pp. 1999-2009
-
-
Wang, H.W.1
Sung, S.S.2
-
34
-
-
0034806777
-
The β-peptide hairpin in solution: Conformational study of a β-hexapeptide in methanol by NMR spectroscopy and MD simulation
-
Daura X, Gademann K, Schäfer H, Jaun B, Seebach D, van Gunsteren WF. The β-peptide hairpin in solution: Conformational study of a β-hexapeptide in methanol by NMR spectroscopy and MD simulation. J. Am. Chem. Soc. 2001; 123: 2393-2404.
-
(2001)
J. Am. Chem. Soc.
, vol.123
, pp. 2393-2404
-
-
Daura, X.1
Gademann, K.2
Schäfer, H.3
Jaun, B.4
Seebach, D.5
van Gunsteren, W.F.6
-
35
-
-
0001095973
-
Energy landscape of a β-hairpin peptide in explicit water studied by multicanonical molecular dynamics
-
Higo J, Galzitskaya OV, Ono S, Nakamura H. Energy landscape of a β-hairpin peptide in explicit water studied by multicanonical molecular dynamics. Chem. Phys. Lett. 2001; 337: 169-175.
-
(2001)
Chem. Phys. Lett.
, vol.337
, pp. 169-175
-
-
Higo, J.1
Galzitskaya, O.V.2
Ono, S.3
Nakamura, H.4
-
36
-
-
0036499409
-
Folding and stability of the three-stranded β-sheet peptide Betanova: Insights from molecular dynamics simulations
-
Colombo G, Roccatano D, Mark AE. Folding and stability of the three-stranded β-sheet peptide Betanova: insights from molecular dynamics simulations. Proteins: Struct. Funct. Genet. 2002; 46: 380-392.
-
(2002)
Proteins: Struct. Funct. Genet.
, vol.46
, pp. 380-392
-
-
Colombo, G.1
Roccatano, D.2
Mark, A.E.3
-
37
-
-
0037093874
-
Direct observation of the folding and unfolding of a β-hairpin in explicit water through computer simulation
-
Wu X, Wang S, Brooks BR. Direct observation of the folding and unfolding of a β-hairpin in explicit water through computer simulation. J. Am. Chem. Soc. 2002; 124: 5282-5283.
-
(2002)
J. Am. Chem. Soc.
, vol.124
, pp. 5282-5283
-
-
Wu, X.1
Wang, S.2
Brooks, B.R.3
-
38
-
-
0003544049
-
-
vdf Hochschulverlag AG an der ETH Zürich and BIOMOS b.v: Zürich, Groningen
-
van Gunsteren WF, Billeter SR, Eising AA, Hünenberger PH, Krüger P, Mark AE, Scott WRP, Tironi IG. Biomolecular Simulation: The GROMOS96 Manual and User Guide. vdf Hochschulverlag AG an der ETH Zürich and BIOMOS b.v: Zürich, Groningen 1996.
-
(1996)
Biomolecular Simulation: The GROMOS96 Manual and User Guide
-
-
van Gunsteren, W.F.1
Billeter, S.R.2
Eising, A.A.3
Hünenberger, P.H.4
Krüger, P.5
Mark, A.E.6
Scott, W.R.P.7
Tironi, I.G.8
-
39
-
-
0034488879
-
Position effect of cross-strand side-chain interactions on β-hairpin formation
-
Santiveri CM, Rico M, Jiménez MA. Position effect of cross-strand side-chain interactions on β-hairpin formation. Protein Sci. 2000; 9: 2151-2160.
-
(2000)
Protein Sci.
, vol.9
, pp. 2151-2160
-
-
Santiveri, C.M.1
Rico, M.2
Jiménez, M.A.3
-
40
-
-
0031454065
-
Cross-strand side-chain interactions versus turn conformation in β-hairpins
-
de Alba E, Rico M, Jiménez MA. Cross-strand side-chain interactions versus turn conformation in β-hairpins. Protein Sci. 1997; 6: 2548-2560.
-
(1997)
Protein Sci.
, vol.6
, pp. 2548-2560
-
-
de Alba, E.1
Rico, M.2
Jiménez, M.A.3
-
41
-
-
0035834063
-
Length-dependent stability and strand length limits in antiparallel β-sheet secondary structure
-
Stanger HE, Syud FA, Espinosa JF, Giriat I, Muir T, Gellman SH. Length-dependent stability and strand length limits in antiparallel β-sheet secondary structure. Proc. Natl Acad. Sci. USA 2001; 98: 12015-12020.
-
(2001)
Proc. Natl. Acad. Sci. USA
, vol.98
, pp. 12015-12020
-
-
Stanger, H.E.1
Syud, F.A.2
Espinosa, J.F.3
Giriat, I.4
Muir, T.5
Gellman, S.H.6
-
42
-
-
0034744426
-
β chemical shifts as a tool to delineate β-hairpin structures in peptides
-
β chemical shifts as a tool to delineate β-hairpin structures in peptides. J. Biomol. NMR 2001; 19: 331-345.
-
(2001)
J. Biomol. NMR
, vol.19
, pp. 331-345
-
-
Santiveri, C.M.1
Rico, M.2
Jimenez, M.A.3
-
43
-
-
0008819754
-
The GROMOS biomolecular simulation program package
-
Scott WRP, Hünenberger PH, Tironi IG, Mark AE, Billeter SR, Fennen J, Torda AE, Huber T, Krüger P, van Gunsteren WF. The GROMOS biomolecular simulation program package. J. Phys. Chem. A 1999; 103: 3596-3607.
-
(1999)
J. Phys. Chem. A
, vol.103
, pp. 3596-3607
-
-
Scott, W.R.P.1
Hünenberger, P.H.2
Tironi, I.G.3
Mark, A.E.4
Billeter, S.R.5
Fennen, J.6
Torda, A.E.7
Huber, T.8
Krüger, P.9
van Gunsteren, W.F.10
-
46
-
-
33750587438
-
Molecular dynamics with coupling to an external bath
-
Berendsen HJC, Postma JPM, van Gunsteren WF, Dinola A, Haak JR. Molecular dynamics with coupling to an external bath. J. Chem. Phys. 1984; 81: 3684-3690.
-
(1984)
J. Chem. Phys.
, vol.81
, pp. 3684-3690
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
van Gunsteren, W.F.3
Dinola, A.4
Haak, J.R.5
-
47
-
-
33646940952
-
Numerical integration of Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
-
Ryckaert JP, Ciccotti G, Berendsen HJC. 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
-
48
-
-
2242491482
-
Consistent dielectric properties of the simple point-charge and extended simple point-charge water models at 277 and 300K
-
Smith PE, van Gunsteren WF. Consistent dielectric properties of the simple point-charge and extended simple point-charge water models at 277 and 300K. J. Chem. Phys. 1994; 100: 3169-3174.
-
(1994)
J. Chem. Phys.
, vol.100
, pp. 3169-3174
-
-
Smith, P.E.1
van Gunsteren, W.F.2
-
49
-
-
0033557181
-
Folding-unfolding thermodynamics of a β-heptapeptide from equilibrium simulations
-
Daura X, van Gunsteren WF, Mark AE. Folding-unfolding thermodynamics of a β-heptapeptide from equilibrium simulations. Proteins: Struct. Funct. Genet. 1999; 34: 269-280.
-
(1999)
Proteins: Struct. Funct. Genet.
, vol.34
, pp. 269-280
-
-
Daura, X.1
van Gunsteren, W.F.2
Mark, A.E.3
-
51
-
-
0020997912
-
Dictionary of protein secondary structure: Pattern-recognition of hydrogen-bonded and geometrical features
-
Kabsch W, Sander C. Dictionary of protein secondary structure: pattern-recognition of hydrogen-bonded and geometrical features. Biopolymers 1983; 22: 2577-2637.
-
(1983)
Biopolymers
, vol.22
, pp. 2577-2637
-
-
Kabsch, W.1
Sander, C.2
-
52
-
-
0026089657
-
Efficient computation of three-dimensional protein structures in solution from nuclear magnetic resonance data using the program DIANA and the supporting programs CALIBA, HABAS and GLOMSA
-
Güntert P, Braun W, Wüthrich K. Efficient computation of three-dimensional protein structures in solution from nuclear magnetic resonance data using the program DIANA and the supporting programs CALIBA, HABAS and GLOMSA. J. Mol. Biol. 1991; 217: 517-530.
-
(1991)
J. Mol. Biol.
, vol.217
, pp. 517-530
-
-
Güntert, P.1
Braun, W.2
Wüthrich, K.3
-
55
-
-
0033624685
-
Fast kinetics and mechanisms in protein folding
-
Eaton WA, Muñoz V, Hagen SJ, Jas GS, Lapidus LJ, Henry ER, Hofrichter J. Fast kinetics and mechanisms in protein folding. Annu. Rev. Biophys. Biomol. Struct. 2000; 29: 327-359.
-
(2000)
Annu. Rev. Biophys. Biomol. Struct.
, vol.29
, pp. 327-359
-
-
Eaton, W.A.1
Muñoz, V.2
Hagen, S.J.3
Jas, G.S.4
Lapidus, L.J.5
Henry, E.R.6
Hofrichter, J.7
-
56
-
-
0036399212
-
Unfolded state of peptides
-
Daura X, Glättli A, Gee P, Peter C, van Gunsteren WF. Unfolded state of peptides. Adv. Prot. Chem. 2002; 62: 341-360.
-
(2002)
Adv. Prot. Chem.
, vol.62
, pp. 341-360
-
-
Daura, X.1
Glättli, A.2
Gee, P.3
Peter, C.4
van Gunsteren, W.F.5
|