-
1
-
-
0347262257
-
Identical short peptide sequences in unrelated proteins can have different conformations: A testing ground for theories of immune recognition
-
Wilson IA, Haft DH, Getzoff ED, Tamer JA, Lemer RA, Brenner S. Identical short peptide sequences in unrelated proteins can have different conformations: a testing ground for theories of immune recognition. Proc. Natl. Acad. Sci. U.S.A. 1985; 82: 5255-5259.
-
(1985)
Proc. Natl. Acad. Sci. U.S.A
, vol.82
, pp. 5255-5259
-
-
Wilson, I.A.1
Haft, D.H.2
Getzoff, E.D.3
Tamer, J.A.4
Lemer, R.A.5
Brenner, S.6
-
2
-
-
0027448801
-
Origins of structural diversity within sequentially identical hexapeptides
-
Cohen BI, Presnell SR, Cohen FE. Origins of structural diversity within sequentially identical hexapeptides. Protein Sci 1993; 2: 2134-2145.
-
(1993)
Protein Sci
, vol.2
, pp. 2134-2145
-
-
Cohen, B.I.1
Presnell, S.R.2
Cohen, F.E.3
-
3
-
-
0001079105
-
On the use of sequence homologies to predict protein structure: Identical pentapeptides can have completely different conformations
-
Kabsch W, Sander C. On the use of sequence homologies to predict protein structure: identical pentapeptides can have completely different conformations. Proc. Natl. Acad. Sci. U.S.A. 1984; 81: 1075-1078.
-
(1984)
Proc. Natl. Acad. Sci. U.S.A
, vol.81
, pp. 1075-1078
-
-
Kabsch, W.1
Sander, C.2
-
4
-
-
0031871068
-
Chameleon sequences in the PDB
-
Mezei M. Chameleon sequences in the PDB. Protein Eng. 1998; 11: 411-414.
-
(1998)
Protein Eng
, vol.11
, pp. 411-414
-
-
Mezei, M.1
-
5
-
-
0034333229
-
An analysis of the helix-to-strand transition between peptides with identical sequence
-
Zhou X, Alber F, Folkers G, Gonnet GH, Chelvanayagam G. An analysis of the helix-to-strand transition between peptides with identical sequence. Proteins 2000; 41: 248-256.
-
(2000)
Proteins
, vol.41
, pp. 248-256
-
-
Zhou, X.1
Alber, F.2
Folkers, G.3
Gonnet, G.H.4
Chelvanayagam, G.5
-
6
-
-
0142241182
-
On the properties and sequence context of structurally ambivalent fragments in proteins
-
Kuznetsov IB, Rackovsky S. On the properties and sequence context of structurally ambivalent fragments in proteins. Protein Sci. 2003; 12: 2420-2433.
-
(2003)
Protein Sci
, vol.12
, pp. 2420-2433
-
-
Kuznetsov, I.B.1
Rackovsky, S.2
-
7
-
-
0029865623
-
Context-dependent secondary structure formation of a designed protein sequence
-
Minor DL Jr, Kim PS. Context-dependent secondary structure formation of a designed protein sequence. Nature 1996; 380: 730-734.
-
(1996)
Nature
, vol.380
, pp. 730-734
-
-
Minor Jr, D.L.1
Kim, P.S.2
-
9
-
-
4444267407
-
Beta-hairpin conformation of fibrillogenic peptides: Structure and alpha-beta transition mechanism revealed by molecular dynamics simulations
-
Daidone I, Simona F, Roccatano D, Broglia RA, Tiana G. Colombo G. Di Nola A. Beta-hairpin conformation of fibrillogenic peptides: structure and alpha-beta transition mechanism revealed by molecular dynamics simulations. Proteins 2004; 57: 198-204.
-
(2004)
Proteins
, vol.57
, pp. 198-204
-
-
Daidone, I.1
Simona, F.2
Roccatano, D.3
Broglia, R.A.4
Tiana, G.5
Colombo, G.6
Di Nola, A.7
-
10
-
-
7744225860
-
Modeling the alpha-helix to beta-hairpin transition mechanism and the formation of oligomeric aggregates of the fibrillogenic peptide Abeta(12-28): Insights from all-atom molecular dynamics simulations
-
Simona F, Tiana G, Broglia RA, Colombo G. Modeling the alpha-helix to beta-hairpin transition mechanism and the formation of oligomeric aggregates of the fibrillogenic peptide Abeta(12-28): insights from all-atom molecular dynamics simulations. J. Mol. Graph. Model. 2004; 23: 263-273.
-
(2004)
J. Mol. Graph. Model
, vol.23
, pp. 263-273
-
-
Simona, F.1
Tiana, G.2
Broglia, R.A.3
Colombo, G.4
-
11
-
-
0036708438
-
Exploring the propensities of helices in PrP(C) to form beta sheet using NMR structures and sequence alignments
-
Dima RI, Thirumalai D. Exploring the propensities of helices in PrP(C) to form beta sheet using NMR structures and sequence alignments. Biophys. J. 2002; 83: 1268-1280.
-
(2002)
Biophys. J
, vol.83
, pp. 1268-1280
-
-
Dima, R.I.1
Thirumalai, D.2
-
12
-
-
0034584899
-
Proteins that convert from alpha helix to beta sheet: Implications for folding and disease
-
Gross M. Proteins that convert from alpha helix to beta sheet: implications for folding and disease. Curr. Protein Pept. Sci. 2000; 1: 339-347.
-
(2000)
Curr. Protein Pept. Sci
, vol.1
, pp. 339-347
-
-
Gross, M.1
-
13
-
-
0029588554
-
High helical propensity of the peptide fragments derived from beta-lactoglobulin, a predominantly beta-sheet protein
-
Hamada D, Kuroda Y, Tanaka T, Goto Y. High helical propensity of the peptide fragments derived from beta-lactoglobulin, a predominantly beta-sheet protein. J. Mol. Biol. 1995; 254: 737-746.
-
(1995)
J. Mol. Biol
, vol.254
, pp. 737-746
-
-
Hamada, D.1
Kuroda, Y.2
Tanaka, T.3
Goto, Y.4
-
14
-
-
0029740071
-
Non-native alpha-helical intermediate in the refolding of beta-lactoglobulin, a predominantly beta-sheet protein
-
Hamada D, Segawa S, Goto Y. Non-native alpha-helical intermediate in the refolding of beta-lactoglobulin, a predominantly beta-sheet protein. Nat. Struct. Biol. 1996; 3: 868-873.
-
(1996)
Nat. Struct. Biol
, vol.3
, pp. 868-873
-
-
Hamada, D.1
Segawa, S.2
Goto, Y.3
-
15
-
-
0030334664
-
High helicity of peptide fragments corresponding to beta-strand regions of betalactoglobulin observed by 2D-NMR spectroscopy
-
Kuroda Y, Hamada D, Tanaka T, Goto Y. High helicity of peptide fragments corresponding to beta-strand regions of betalactoglobulin observed by 2D-NMR spectroscopy. Fold. Des. 1996; 1: 255-263.
-
(1996)
Fold. Des
, vol.1
, pp. 255-263
-
-
Kuroda, Y.1
Hamada, D.2
Tanaka, T.3
Goto, Y.4
-
16
-
-
0028053187
-
Understanding how proteins fold: The lysozyme story so far
-
Dobson CM, Evans PA, Radford SE. Understanding how proteins fold: the lysozyme story so far. Trends Biochem. Sci. 1994; 19: 31-37.
-
(1994)
Trends Biochem. Sci
, vol.19
, pp. 31-37
-
-
Dobson, C.M.1
Evans, P.A.2
Radford, S.E.3
-
17
-
-
0024413264
-
Water-inserted alpha-helical segments implicate reverse turns as folding intermediates
-
Sundaralingam M, Sekharudu YC. Water-inserted alpha-helical segments implicate reverse turns as folding intermediates. Science 1989; 244: 1333-1337.
-
(1989)
Science
, vol.244
, pp. 1333-1337
-
-
Sundaralingam, M.1
Sekharudu, Y.C.2
-
18
-
-
0038241788
-
Conformational dynamics of trialanine in water. 2. Comparison of AMBER, CHARMM, GROMOS, and OPLS force fields to NMR and infrared experiments
-
Mu Y, Kosov D, Stock G. Conformational dynamics of trialanine in water. 2. Comparison of AMBER, CHARMM, GROMOS, and OPLS force fields to NMR and infrared experiments. J. Phys. Chem. B 2003; 107: 5064-5073.
-
(2003)
J. Phys. Chem. B
, vol.107
, pp. 5064-5073
-
-
Mu, Y.1
Kosov, D.2
Stock, G.3
-
19
-
-
0034818192
-
Isotope-edited two-dimensional vibrational spectroscopy of a short alpha-helix in water
-
Woutersen S, Hamm P. Isotope-edited two-dimensional vibrational spectroscopy of a short alpha-helix in water. J. Chem. Phys. 2001: 114: 2727-2737.
-
(2001)
J. Chem. Phys
, vol.114
, pp. 2727-2737
-
-
Woutersen, S.1
Hamm, P.2
-
20
-
-
0037021502
-
Tripeptides adopt stable structures in water. A combined polarized visible Raman, FTIR, and VCD spectroscopy study
-
Eker F, Cao X, Nafie L, Schweitzer-Stenner R. Tripeptides adopt stable structures in water. A combined polarized visible Raman, FTIR, and VCD spectroscopy study. J. Am. Chem. Soc. 2002; 124: 14330-14341.
-
(2002)
J. Am. Chem. Soc
, vol.124
, pp. 14330-14341
-
-
Eker, F.1
Cao, X.2
Nafie, L.3
Schweitzer-Stenner, R.4
-
21
-
-
0037047134
-
Polyproline II structure in a sequence of seven alanine residues
-
Shi Z, Olson CA, Rose GD, Baldwin RL, Kallenbach NR. Polyproline II structure in a sequence of seven alanine residues. Proc. Natl. Acad. Sci. U.S.A. 2002; 99: 9190-9195.
-
(2002)
Proc. Natl. Acad. Sci. U.S.A
, vol.99
, pp. 9190-9195
-
-
Shi, Z.1
Olson, C.A.2
Rose, G.D.3
Baldwin, R.L.4
Kallenbach, N.R.5
-
22
-
-
1842500993
-
Unfolded state of polyalanine is a segmented polyproline II helix
-
Kentsis A, Mezei M, Gindin T, Osman R. Unfolded state of polyalanine is a segmented polyproline II helix. Proteins 2004; 55: 493-501.
-
(2004)
Proteins
, vol.55
, pp. 493-501
-
-
Kentsis, A.1
Mezei, M.2
Gindin, T.3
Osman, R.4
-
23
-
-
1842500992
-
Polyproline II helix is the preferred conformation for unfolded polyalanine in water
-
Mezei M, Fleming PJ, Srinivasan R, Rose GD. Polyproline II helix is the preferred conformation for unfolded polyalanine in water. Proteins 2004; 55: 502-507.
-
(2004)
Proteins
, vol.55
, pp. 502-507
-
-
Mezei, M.1
Fleming, P.J.2
Srinivasan, R.3
Rose, G.D.4
-
24
-
-
0031473847
-
SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling
-
Guex N, Peitsch MC. SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis 1997; 18: 2714-2723.
-
(1997)
Electrophoresis
, vol.18
, pp. 2714-2723
-
-
Guex, N.1
Peitsch, M.C.2
-
25
-
-
0002775934
-
Interaction models for water in relation to protein hydration
-
Pullman B ed, Reidel Publishing Company Dordrecht: The Netherlands
-
Berendsen HJC, Postma JPM, van Gunsteren WF, Hermans J. Interaction models for water in relation to protein hydration. In Inter Molecular Forces, Pullman B (ed). Reidel Publishing Company Dordrecht: The Netherlands. 1981; 331-342.
-
(1981)
Inter Molecular Forces
, pp. 331-342
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
van Gunsteren, W.F.3
Hermans, J.4
-
26
-
-
33846823909
-
Particle mesh Ewald: An N-log(N) method for Ewald sums in large systems
-
Darden T, York D, Pedersen L. Particle mesh Ewald: an N-log(N) method for Ewald sums in large systems. J. Chem. Phys. 1993; 98: 10089-10092.
-
(1993)
J. Chem. Phys
, vol.98
, pp. 10089-10092
-
-
Darden, T.1
York, D.2
Pedersen, L.3
-
27
-
-
33645961739
-
A smooth particle mesh Ewald method
-
Essmann U, Perera L, Berkowitz M, Darden T, Lee H, Pedersen L. 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.3
Darden, T.4
Lee, H.5
Pedersen, L.6
-
29
-
-
33750587438
-
Molecular dynamics with coupling to an external bath
-
Berendsen H, Postma J, DiNola A, Haak J. 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.1
Postma, J.2
DiNola, A.3
Haak, J.4
-
30
-
-
0035789518
-
Gromacs 3.0: A package for molecular simulation and trajectory analysis
-
Lindahl E, Hess B, van der Spoel D. Gromacs 3.0: A package for molecular simulation and trajectory analysis. J. Mol. Model. 2001; 7: 306-317.
-
(2001)
J. Mol. Model
, vol.7
, pp. 306-317
-
-
Lindahl, E.1
Hess, B.2
van der Spoel, D.3
-
31
-
-
0003544049
-
-
vdf Hochschulverlag AG an der ETH: 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, 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
-
32
-
-
0008819754
-
The GROMOS biomolecular simulation program package
-
Scott WRP, Huenenberger P, Tironi I, Mark A, Billeter S, Fennen J, Torda A, Huber T, Krueger P, van Gunsteren W. 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
Huenenberger, P.2
Tironi, I.3
Mark, A.4
Billeter, S.5
Fennen, J.6
Torda, A.7
Huber, T.8
Krueger, P.9
van Gunsteren, W.10
-
33
-
-
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
-
35
-
-
0034137209
-
Conformational features of a hexapeptide model Ac-TGAAKA-NH2 corresponding to a hydrated alpha helical segment from glyceraldehyde 3-phosphate dehydrogenase: Implications for the role of turns in helix folding
-
Sasidhar YU, Ramakrishna V. Conformational features of a hexapeptide model Ac-TGAAKA-NH2 corresponding to a hydrated alpha helical segment from glyceraldehyde 3-phosphate dehydrogenase: implications for the role of turns in helix folding. Indian J. Biochem. Biophys. 2000; 37: 34-44.
-
(2000)
Indian J. Biochem. Biophys
, vol.37
, pp. 34-44
-
-
Sasidhar, Y.U.1
Ramakrishna, V.2
-
36
-
-
0026768829
-
Folding of peptide fragments comprising the complete sequence of proteins. Models for initiation of protein folding. I. Myohemerythrin
-
Dyson HJ, Meruntka G, Waltho JP, Lerner RA, Wright PE. Folding of peptide fragments comprising the complete sequence of proteins. Models for initiation of protein folding. I. Myohemerythrin. J. Mol. Biol. 1992; 226: 795-817.
-
(1992)
J. Mol. Biol
, vol.226
, pp. 795-817
-
-
Dyson, H.J.1
Meruntka, G.2
Waltho, J.P.3
Lerner, R.A.4
Wright, P.E.5
-
37
-
-
0035932703
-
Helix folding of an alanine-based peptide in explicit water
-
Wu X, Wang S. Helix folding of an alanine-based peptide in explicit water. J. Phys. Chem. B 2001; 105: 2227-2235.
-
(2001)
J. Phys. Chem. B
, vol.105
, pp. 2227-2235
-
-
Wu, X.1
Wang, S.2
-
38
-
-
27744545833
-
Mechanism of helix nucleation and propagation: Microscopic view from microsecond time scale MD simulations
-
Monticelli L, Tieleman DP. Colombo G. Mechanism of helix nucleation and propagation: Microscopic view from microsecond time scale MD simulations. J. Phys. Chem. B 2005; 109: 20064.
-
(2005)
J. Phys. Chem. B
, vol.109
, pp. 20064
-
-
Monticelli, L.1
Tieleman, D.P.2
Colombo, G.3
-
39
-
-
0037423747
-
Sequence and structure patterns in proteins from an analysis of the shortest helices: Implications for helix nucleation
-
Pal L, Chakrabarti P, Basu G. Sequence and structure patterns in proteins from an analysis of the shortest helices: implications for helix nucleation. J. Mol. Biol. 2003; 328: 273-291.
-
(2003)
J. Mol. Biol
, vol.328
, pp. 273-291
-
-
Pal, L.1
Chakrabarti, P.2
Basu, G.3
-
40
-
-
0030006074
-
Molecular dynamics simulations of synthetic peptide folding
-
Sung SS. Wu XW. Molecular dynamics simulations of synthetic peptide folding. Proteins 1996; 25: 202-214.
-
(1996)
Proteins
, vol.25
, pp. 202-214
-
-
Sung, S.W.X.1
-
41
-
-
0028200975
-
Helix folding simulations with various initial conformations
-
Sung SS. Helix folding simulations with various initial conformations. Biophys. J. 1994; 66: 1796-1803.
-
(1994)
Biophys. J
, vol.66
, pp. 1796-1803
-
-
Sung, S.S.1
-
42
-
-
0032906553
-
Carlo simulations of beta-hairpin folding at constant temperature
-
Sung SS. Monte Carlo simulations of beta-hairpin folding at constant temperature. Biophys. J. 1999; 76: 164-175.
-
(1999)
Biophys. J
, vol.76
, pp. 164-175
-
-
Monte, S.S.S.1
-
43
-
-
3342963982
-
Detecting hidden sequence propensity for amyloid fibril formation
-
Yoon S, Welsh WJ. Detecting hidden sequence propensity for amyloid fibril formation. Protein Sci. 2004; 13: 2149-2160.
-
(2004)
Protein Sci
, vol.13
, pp. 2149-2160
-
-
Yoon, S.1
Welsh, W.J.2
-
44
-
-
0141480850
-
Mechanism for the alpha-helix to beta-hairpin transition
-
Ding F, Borreguero JM, Buldyrey SV, Stanley HE, Dokholyan NV. Mechanism for the alpha-helix to beta-hairpin transition. Proteins 2003; 53: 220-228.
-
(2003)
Proteins
, vol.53
, pp. 220-228
-
-
Ding, F.1
Borreguero, J.M.2
Buldyrey, S.V.3
Stanley, H.E.4
Dokholyan, N.V.5
-
45
-
-
0022423920
-
Theory for the folding and stability of globular proteins
-
Dill KA. Theory for the folding and stability of globular proteins. Biochemistry 1985; 24: 1501-1509.
-
(1985)
Biochemistry
, vol.24
, pp. 1501-1509
-
-
Dill, K.A.1
-
46
-
-
0028929556
-
Principles of protein folding-a perspective from simple exact models
-
Dill KA, Bromberg S, Yue K, Fiebig KM, Yee DP, Thomas PD, Chan HS. Principles of protein folding-a perspective from simple exact models. Protein Sci. 1995; 4: 561-602.
-
(1995)
Protein Sci
, vol.4
, pp. 561-602
-
-
Dill, K.A.1
Bromberg, S.2
Yue, K.3
Fiebig, K.M.4
Yee, D.P.5
Thomas, P.D.6
Chan, H.S.7
-
47
-
-
0025370815
-
Dominant forces in protein folding
-
Dill KA. Dominant forces in protein folding. Biochemistry 1990; 29: 7133-7155.
-
(1990)
Biochemistry
, vol.29
, pp. 7133-7155
-
-
Dill, K.A.1
|