-
1
-
-
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
-
2
-
-
0033556236
-
Peptide folding: When simulation meets experiment
-
Daura X, Gademann K, Jaun B, Seebach D, van Gunsteren WF, Mark AE. Peptide folding: when simulation meets experiment. Angew. Chem. Int. Ed. 1999; 38: 236-240.
-
(1999)
Angew Chem. Int. Ed.
, vol.38
, pp. 236-240
-
-
Daura, X.1
Gademann, K.2
Jaun, B.3
Seebach, D.4
van Gunsteren, W.F.5
Mark, A.E.6
-
3
-
-
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
-
4
-
-
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 HJC. 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.C.4
-
5
-
-
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
-
6
-
-
0035910479
-
The key to solving the protein-folding problem lies in an accurate description of the denatured state
-
van Gunsteren WF, Bürgi R, Peter C, Daura X. The key to solving the protein-folding problem lies in an accurate description of the denatured state. Angew. Chem. Int. Ed. 2001; 40: 351-355.
-
(2001)
Angew Chem. Int. Ed.
, vol.40
, pp. 351-355
-
-
van Gunsteren, W.F.1
Bürgi, R.2
Peter, C.3
Daura, X.4
-
7
-
-
0037032269
-
Can one derive the conformational preference of a β-peptide from its CD spectrum?
-
Glättli A, Daura X, Seebach D, van Gunsteren WF. Can one derive the conformational preference of a β-peptide from its CD spectrum? J. Am. Chem. Soc. 2002; 124: 12 972-12 978.
-
(2002)
J. Am. Chem. Soc.
, vol.124
, pp. 12972-12978
-
-
Glättli, A.1
Daura, X.2
Seebach, D.3
van Gunsteren, W.F.4
-
8
-
-
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
-
9
-
-
0037093874
-
Direct observation of the folding and unfolding of a β-hairpin in explicit water through computer simulation
-
Wu HW, Wang SM, Brooks HR. 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, H.W.1
Wang, S.M.2
Brooks, H.R.3
-
10
-
-
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
-
11
-
-
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
, pp. 10780-10785
-
-
Ferrara, P.1
Caflisch, A.2
-
12
-
-
0037397987
-
Peptide folding simulations
-
Gnanakaran S, Nymeyer H, Portman J, Sanbonmatsu KY, Garcia AE. Peptide folding simulations. Curr. Opin. Struct. Biol. 2003; 134: 168-174.
-
(2003)
Curr. Opin. Struct. Biol.
, vol.134
, pp. 168-174
-
-
Gnanakaran, S.1
Nymeyer, H.2
Portman, J.3
Sanbonmatsu, K.Y.4
Garcia, A.E.5
-
14
-
-
0033529908
-
Molecular dynamics simulations of unfolding and refolding of a β-hairpin fragment of protein G
-
Pande VS, Rokhsar DS. Molecular dynamics simulations of unfolding and refolding of a 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
-
15
-
-
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
, pp. 11258-11259
-
-
Simmerling, C.1
Strockbine, B.2
Roitberg, A.E.3
-
16
-
-
0037038372
-
Absolute comparison of simulated and experimental protein-folding dynamics
-
Snow CD, Nguyen N, 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, N.2
Pande, V.S.3
Gruebele, M.4
-
17
-
-
0032705432
-
Designed molecules that fold to mimic protein secondary structures
-
Stigers KD, Soth MJ, Nowick JS. Designed molecules that fold to mimic protein secondary structures. Curr. Opin. Chem. Biol. 1999; 3: 714-723.
-
(1999)
Curr. Opin. Chem. Biol.
, vol.3
, pp. 714-723
-
-
Stigers, K.D.1
Soth, M.J.2
Nowick, J.S.3
-
18
-
-
0035587799
-
Models of higher-order structure: Foldamers and beyond
-
Cubberley MS, Iverson BL. Models of higher-order structure: foldamers and beyond. Curr. Opin. Chem. Biol. 2001; 5: 650-653.
-
(2001)
Curr. Opin. Chem. Biol.
, vol.5
, pp. 650-653
-
-
Cubberley, M.S.1
Iverson, B.L.2
-
19
-
-
0035542909
-
A field guide to foldamers
-
Hill DJ, Mio MJ, Prince RB, Hughes TS, Moore JS. A field guide to foldamers. Chem. Rev. 2001; 101: 3893-4011.
-
(2001)
Chem. Rev.
, vol.101
, pp. 3893-4011
-
-
Hill, D.J.1
Mio, M.J.2
Prince, R.B.3
Hughes, T.S.4
Moore, J.S.5
-
20
-
-
0032700369
-
Designing secondary structures: 5-azidomethyl tetrahydrofuran-2-carboxylates as carbohydrate-derived dipeptide isosteres
-
Smith MD, Fleet GWJ. Designing secondary structures: 5-azidomethyl tetrahydrofuran-2-carboxylates as carbohydrate-derived dipeptide isosteres. J. Peptide Sci. 1999; 5: 425-441.
-
(1999)
J. Peptide Sci.
, vol.5
, pp. 425-441
-
-
Smith, M.D.1
Fleet, G.W.J.2
-
22
-
-
0344515255
-
Secondary structure in oligomers of carbohydrate amino acids
-
Smith MD, Claridge TDW, Tranter GE, Sansom MSP, Fleet GWJ. Secondary structure in oligomers of carbohydrate amino acids. Chem. Commun. 1998; 2041-2042.
-
(1998)
Chem. Commun.
, pp. 2041-2042
-
-
Smith, M.D.1
Claridge, T.D.W.2
Tranter, G.E.3
Sansom, M.S.P.4
Fleet, G.W.J.5
-
23
-
-
0033548560
-
Absence of secondary structure in a carbopeptoid tetramer of a trans-5-aminomethyl-tetrahydrofuran-2-carboxylate
-
Smith MD, Long DD, Martin A, Marquess DG, Claridge TDW, Fleet GWJ. Absence of secondary structure in a carbopeptoid tetramer of a trans-5-aminomethyl-tetrahydrofuran-2-carboxylate. Tetrahedron Lett. 1999; 40: 2191-2194.
-
(1999)
Tetrahedron Lett.
, vol.40
, pp. 2191-2194
-
-
Smith, M.D.1
Long, D.D.2
Martin, A.3
Marquess, D.G.4
Claridge, T.D.W.5
Fleet, G.W.J.6
-
24
-
-
0033548539
-
An octameric carbopeptoid; Secondary structure in octameric and tetrameric 5-aminomethyl-tetrahydrofuran-2-carboxylates
-
Claridge TDW, Long DD, Hungerford NL, Aplin RT, Smith MD, Marquess DG, Fleet GWJ. An octameric carbopeptoid; Secondary structure in octameric and tetrameric 5-aminomethyl-tetrahydrofuran-2-carboxylates. Tetrahedron Lett. 1999; 40: 2199-2202.
-
(1999)
Tetrahedron Lett.
, vol.40
, pp. 2199-2202
-
-
Claridge, T.D.W.1
Long, D.D.2
Hungerford, N.L.3
Aplin, R.T.4
Smith, M.D.5
Marquess, D.G.6
Fleet, G.W.J.7
-
25
-
-
4544386044
-
Carbopeptoid folding: Effects of stereochemistry, chain length and solvent
-
Baron R, Bakowics D, van Gunsteren WF. Carbopeptoid folding: effects of stereochemistry, chain length and solvent. Angew. Chem. Int. Ed. 2004; 43: 4055-4059.
-
(2004)
Angew. Chem. Int. Ed.
, vol.43
, pp. 4055-4059
-
-
Baron, R.1
Bakowics, D.2
van Gunsteren, W.F.3
-
26
-
-
0003544051
-
-
Vdf Hochschulverlag AG: Zürich
-
van Gunsteren WF, Billeter SR, Eising AA, Hünenberger PH, Krüger P, Mark AE, Scott WRP, Tironi IG. The GROMOS96 Manual and User Guide. Vdf Hochschulverlag AG: Zürich, 1996.
-
(1996)
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
-
27
-
-
0035425883
-
An improved GROMOS96 force field for aliphatic hydrocarbons in the condensed phase
-
Schuler LD, Daura X, van Gunsteren WF. An improved GROMOS96 force field for aliphatic hydrocarbons in the condensed phase. J. Comput. Chem. 2001; 22: 1205-1218.
-
(2001)
J. Comput. Chem.
, vol.22
, pp. 1205-1218
-
-
Schuler, L.D.1
Daura, X.2
van Gunsteren, W.F.3
-
28
-
-
0037569250
-
A consistent potential energy parameter set for lipids: Dipalmitoylphosphatidylcholine as a benchmark of the GROMOS96 45A3 force field
-
Chandrasekhar I, Kastenholz M, Lins RD, Oostenbrink C, Schuler LD, Tieleman DP, van Gunsteren WF. A consistent potential energy parameter set for lipids: dipalmitoylphosphatidylcholine as a benchmark of the GROMOS96 45A3 force field. Eur. Biophys. J. 2003; 32: 67-77.
-
(2003)
Eur. Biophys. J.
, vol.32
, pp. 67-77
-
-
Chandrasekhar, I.1
Kastenholz, M.2
Lins, R.D.3
Oostenbrink, C.4
Schuler, L.D.5
Tieleman, D.P.6
van Gunsteren, W.F.7
-
29
-
-
84946655114
-
A molecular dynamics simulation study of chloroform
-
Tironi IG, van Gunsteren WF. A molecular dynamics simulation study of chloroform. Mol. Phys. 1994; 83: 381-403.
-
(1994)
Mol. Phys.
, vol.83
, pp. 381-403
-
-
Tironi, I.G.1
van Gunsteren, W.F.2
-
30
-
-
0000454818
-
A force field for liquid dimethyl sulfoxide and physical properties of liquid dimethyl sulfoxide calculated using molecular dynamics simulations
-
Liu H, Müller-Plathe F, van Gunsteren WF. A force field for liquid dimethyl sulfoxide and physical properties of liquid dimethyl sulfoxide calculated using molecular dynamics simulations. J. Am. Chem. Soc. 1995; 117: 4363-4366.
-
(1995)
J. Am. Chem. Soc.
, vol.117
, pp. 4363-4366
-
-
Liu, H.1
Müller-Plathe, F.2
van Gunsteren, W.F.3
-
31
-
-
0000184330
-
Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
-
Ryckaert J-P, Ciccotti G, Berendsen HJC. Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J. Comput. Chem. 1977; 81: 3684-3698.
-
(1977)
J. Comput. Chem.
, vol.81
, pp. 3684-3698
-
-
Ryckaert, J.-P.1
Ciccotti, G.2
Berendsen, H.J.C.3
-
32
-
-
33750587438
-
Molecular dynamics with coupling to an external bath
-
Berendsen HJC, Postma JPM, van Gunsteren WF, Di Nola A, Haak JR. Molecular dynamics with coupling to an external bath. J. Chem. Phys. 1984; 81: 3684-3698.
-
(1984)
J. Chem. Phys.
, vol.81
, pp. 3684-3698
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
van Gunsteren, W.F.3
Di Nola, A.4
Haak, J.R.5
-
33
-
-
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
-
34
-
-
0036939031
-
β-peptides with different secondary-structure preferences: How different are their conformational spaces?
-
Baron R, Bakowies D, van Gunsteren WF, Daura X. β-peptides with different secondary-structure preferences: how different are their conformational spaces? Helv. Chim. Acta 2002; 85: 3872-3882.
-
(2002)
Helv. Chim. Acta
, vol.85
, pp. 3872-3882
-
-
Baron, R.1
Bakowies, D.2
van Gunsteren, W.F.3
Daura, X.4
-
35
-
-
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
-
36
-
-
0034323089
-
Absolute entropies from molecular dynamics simulation trajectories
-
Schäfer H, Mark AE, van Gunsteren WF. Absolute entropies from molecular dynamics simulation trajectories. J. Chem. Phys. 2000; 113: 7809-7817.
-
(2000)
J. Chem. Phys.
, vol.113
, pp. 7809-7817
-
-
Schäfer, H.1
Mark, A.E.2
van Gunsteren, W.F.3
-
37
-
-
0035314075
-
Entropy calculations on a reversibly folding peptide: Changes in solute free energy cannot explain folding behavior
-
Schäfer H, Daura X, Mark AE, van Gunsteren WF. Entropy calculations on a reversibly folding peptide: changes in solute free energy cannot explain folding behavior. Proteins Struct. Funct. Genet. 2001; 43: 45-56.
-
(2001)
Proteins Struct. Funct. Genet.
, vol.43
, pp. 45-56
-
-
Schäfer, H.1
Daura, X.2
Mark, A.E.3
van Gunsteren, W.F.4
-
39
-
-
0036467064
-
Entropy calculations on the molten globule state of a protein: Side-chain entropies of α-lactalbumin
-
Schäfer H, Smith LJ, Mark AE, van Gunsteren WF. Entropy calculations on the molten globule state of a protein: side-chain entropies of α-lactalbumin. Prot. Struct. Funct. Genet. 2002; 46: 215-224.
-
(2002)
Prot. Struct. Funct. Genet.
, vol.46
, pp. 215-224
-
-
Schäfer, H.1
Smith, L.J.2
Mark, A.E.3
van Gunsteren, W.F.4
|