-
1
-
-
0031851978
-
Equilibrium NMR studies of unfolded and partially folded proteins
-
Dyson HJ, Wright PE (1998) Equilibrium NMR studies of unfolded and partially folded proteins. Nat Struct Biol 5 (Supplement): 499-503.
-
(1998)
Nat Struct Biol
, vol.5
, Issue.SUPPL.
, pp. 499-503
-
-
Dyson, H.J.1
Wright, P.E.2
-
2
-
-
0026768829
-
Folding of peptide fragments comprising the complete sequence of proteins. Models for initiation of protein folding. I. Myohemerythrin
-
Dyson HJ, Merutka G, Waltho JP, Lerner RA, Wright PE (1992) Folding of peptide fragments comprising the complete sequence of proteins. Models for initiation of protein folding. I. Myohemerythrin. J Mol Biol 226: 795-817.
-
(1992)
J Mol Biol
, vol.226
, pp. 795-817
-
-
Dyson, H.J.1
Merutka, G.2
Waltho, J.P.3
Lerner, R.A.4
Wright, P.E.5
-
3
-
-
0027248899
-
Peptide models of protein folding initiation sites. 3. The G-H helical hairpin of myoglobin
-
Shin HC, Merutka G, Waltho JP, Tennant LL, Dyson HJ, Wright PE (1993) Peptide models of protein folding initiation sites. 3. The G-H helical hairpin of myoglobin. Biochemistry 32: 6356-6364.
-
(1993)
Biochemistry
, vol.32
, pp. 6356-6364
-
-
Shin, H.C.1
Merutka, G.2
Waltho, J.P.3
Tennant, L.L.4
Dyson, H.J.5
Wright, P.E.6
-
4
-
-
0027165688
-
Peptide models of protein folding initiation sites. 1. Secondary structure formation by peptides corresponding to the G- and H-helices of myoglobin
-
Waltho JP, Feher VA, Merutka G, Dyson HJ, Wright PE (1993) Peptide models of protein folding initiation sites. 1. Secondary structure formation by peptides corresponding to the G- and H-helices of myoglobin. Biochemistry 32: 6337-6347.
-
(1993)
Biochemistry
, vol.32
, pp. 6337-6347
-
-
Waltho, J.P.1
Feher, V.A.2
Merutka, G.3
Dyson, H.J.4
Wright, P.E.5
-
5
-
-
0040589805
-
Conformational analysis of peptides corresponding to all the secondary structure elements of protein L B1 domain: Secondary structure propensities are not conserved in proteins with the same fold
-
Ramirez-Alvarado M, Serrano L, Blanco FJ (1997) Conformational analysis of peptides corresponding to all the secondary structure elements of protein L B1 domain: Secondary structure propensities are not conserved in proteins with the same fold. Protein Sci 6: 162-174.
-
(1997)
Protein Sci
, vol.6
, pp. 162-174
-
-
Ramirez-Alvarado, M.1
Serrano, L.2
Blanco, F.J.3
-
6
-
-
0034696675
-
Native and non-native secondary structure and dynamics in the pH 4 intermediate of apomyoglobin
-
Eliezer D, Chung J, Dyson HJ, Wright PE (2000) Native and non-native secondary structure and dynamics in the pH 4 intermediate of apomyoglobin. Biochemistry 39: 2894-2901.
-
(2000)
Biochemistry
, vol.39
, pp. 2894-2901
-
-
Eliezer, D.1
Chung, J.2
Dyson, H.J.3
Wright, P.E.4
-
7
-
-
3242789489
-
Structural characterization of unfolded states of apomyoglobin using residual dipolar couplings
-
Mohana-Borges R, Goto NK, Kroon GJ, Dyson HJ, Wright PE (2004) Structural characterization of unfolded states of apomyoglobin using residual dipolar couplings. J Mol Biol 340: 1131-1142.
-
(2004)
J Mol Biol
, vol.340
, pp. 1131-1142
-
-
Mohana-Borges, R.1
Goto, N.K.2
Kroon, G.J.3
Dyson, H.J.4
Wright, P.E.5
-
8
-
-
0024707204
-
Unusually stable helix formation in short alanine-based peptides
-
U S A
-
Marqusee S, Robbins VH, Baldwin RL (1989) Unusually stable helix formation in short alanine-based peptides. Proc Natl Acad Sci U S A 86: 5286-5290.
-
(1989)
Proc Natl Acad Sci
, vol.86
, pp. 5286-5290
-
-
Marqusee, S.1
Robbins, V.H.2
Baldwin, R.L.3
-
9
-
-
0028447768
-
Elucidating the folding problem of helical peptides using empirical parameters
-
Munoz V, Serrano L (1994) Elucidating the folding problem of helical peptides using empirical parameters. Nat Struct Biol 1: 399-409.
-
(1994)
Nat Struct Biol
, vol.1
, pp. 399-409
-
-
Munoz, V.1
Serrano, L.2
-
10
-
-
0028500779
-
A short linear peptide that folds into a native stable beta-hairpin in aqueous solution
-
Blanco FJ, Rivas G, Serrano L (1994) A short linear peptide that folds into a native stable beta-hairpin in aqueous solution. Nat Struct Biol 1: 584-590.
-
(1994)
Nat Struct Biol
, vol.1
, pp. 584-590
-
-
Blanco, F.J.1
Rivas, G.2
Serrano, L.3
-
11
-
-
0028865129
-
A short linear peptide derived from the N-terminal sequence of ubiquitin folds into a water-stable non-native beta-hairpin
-
Searle MS, Williams DH, Packman LC (1995) A short linear peptide derived from the N-terminal sequence of ubiquitin folds into a water-stable non-native beta-hairpin. Nat Struct Biol 2: 999-1006.
-
(1995)
Nat Struct Biol
, vol.2
, pp. 999-1006
-
-
Searle, M.S.1
Williams, D.H.2
Packman, L.C.3
-
12
-
-
0033028620
-
Autonomous folding of a peptide corresponding to the N-terminal beta-hairpin from ubiquitin
-
Zerella R, Evans PA, Ionides JM, Packman LC, Trotter BW, Mackay JP, Williams DH (1999) Autonomous folding of a peptide corresponding to the N-terminal beta-hairpin from ubiquitin. Protein Sci 8: 1320-1331.
-
(1999)
Protein Sci
, vol.8
, pp. 1320-1331
-
-
Zerella, R.1
Evans, P.A.2
Ionides, J.M.3
Packman, L.C.4
Trotter, B.W.5
Mackay, J.P.6
Williams, D.H.7
-
13
-
-
0035936697
-
Interplay between hydrophobic cluster and loop propensity in beta-hairpin formation
-
Espinosa JF, Munoz V, Gellman SH (2001) Interplay between hydrophobic cluster and loop propensity in beta-hairpin formation. J Mol Biol 306: 397-402.
-
(2001)
J Mol Biol
, vol.306
, pp. 397-402
-
-
Espinosa, J.F.1
Munoz, V.2
Gellman, S.H.3
-
14
-
-
0038385501
-
Role of local sequence in the folding of cellular retinoic abinding protein I: Structural propensities of reverse turns
-
Rotondi KS, Gierasch LM (2003) Role of local sequence in the folding of cellular retinoic abinding protein I: Structural propensities of reverse turns. Biochemistry 42: 7976-7985.
-
(2003)
Biochemistry
, vol.42
, pp. 7976-7985
-
-
Rotondi, K.S.1
Gierasch, L.M.2
-
15
-
-
0000929505
-
The hydrophobic moment detects periodicity in protein hydrophobicity
-
U S A
-
Eisenberg D, Weiss RM, Terwilliger TC (1984) The hydrophobic moment detects periodicity in protein hydrophobicity. Proc Natl Acad Sci U S A 81: 140-144.
-
(1984)
Proc Natl Acad Sci
, vol.81
, pp. 140-144
-
-
Eisenberg, D.1
Weiss, R.M.2
Terwilliger, T.C.3
-
16
-
-
23444436172
-
Protein design by binary patterning of polar and nonpolar amino acids
-
Kamtekar S, Schiffer JM, Xiong H, Babik JM, Hecht MH (1993) Protein design by binary patterning of polar and nonpolar amino acids. Science 262: 1680-1685.
-
(1993)
Science
, vol.262
, pp. 1680-1685
-
-
Kamtekar, S.1
Schiffer, J.M.2
Xiong, H.3
Babik, J.M.4
Hecht, M.H.5
-
17
-
-
0029898244
-
Global properties of the mapping between local amino acid sequence and local structure in proteins
-
U S A
-
Han KF, Baker D (1996) Global properties of the mapping between local amino acid sequence and local structure in proteins. Proc Natl Acad Sci U S A 93: 5814-5818.
-
(1996)
Proc Natl Acad Sci
, vol.93
, pp. 5814-5818
-
-
Han, K.F.1
Baker, D.2
-
19
-
-
0032555696
-
Prediction of local structure in proteins using a library of sequence-structure motifs
-
Bystroff C, Baker D (1998) Prediction of local structure in proteins using a library of sequence-structure motifs. J Mol Biol 281: 565-577.
-
(1998)
J Mol Biol
, vol.281
, pp. 565-577
-
-
Bystroff, C.1
Baker, D.2
-
20
-
-
0034710871
-
Anatomy of protein structures: Visualizing how a one-dimensional protein chain folds into a three-dimensional shape
-
U S A
-
Tsai CJ, Maizel JV Jr, Nussinov R (2000) Anatomy of protein structures: Visualizing how a one-dimensional protein chain folds into a three-dimensional shape. Proc Natl Acad Sci U S A 97: 12038-12043.
-
(2000)
Proc Natl Acad Sci
, vol.97
, pp. 12038-12043
-
-
Tsai, C.J.1
Maizel Jr., J.V.2
Nussinov, R.3
-
21
-
-
0036406112
-
Small libraries of protein fragments model native protein structures accurately
-
Kolodny R, Koehl P, Guibas L, Levitt M (2002) Small libraries of protein fragments model native protein structures accurately. J Mol Biol 323: 297-307.
-
(2002)
J Mol Biol
, vol.323
, pp. 297-307
-
-
Kolodny, R.1
Koehl, P.2
Guibas, L.3
Levitt, M.4
-
22
-
-
1842635567
-
Clustering of protein structural fragments reveals modular building block approach of nature
-
Tendulkar AV, Joshi AA, Sohoni MA, Wangikar PP (2004) Clustering of protein structural fragments reveals modular building block approach of nature. J Mol Biol 338: 611-629.
-
(2004)
J Mol Biol
, vol.338
, pp. 611-629
-
-
Tendulkar, A.V.1
Joshi, A.A.2
Sohoni, M.A.3
Wangikar, P.P.4
-
23
-
-
0242299187
-
Predictions without templates: New folds, secondary structure, and contacts in CASP5
-
Aloy P, Stark A, Hadley C, Russell RB (2003) Predictions without templates: New folds, secondary structure, and contacts in CASP5. Proteins 53 (Supplement 6):: 436-456.
-
(2003)
Proteins
, vol.53
, Issue.6 SUPPL.
, pp. 436-456
-
-
Aloy, P.1
Stark, A.2
Hadley, C.3
Russell, R.B.4
-
24
-
-
20444484434
-
A decade of CASP: Progress, bottlenecks and prognosis in protein structure prediction
-
Moult J (2005) A decade of CASP: Progress, bottlenecks and prognosis in protein structure prediction. Curr Opin Struct Biol 15: 285-289.
-
(2005)
Curr Opin Struct Biol
, vol.15
, pp. 285-289
-
-
Moult, J.1
-
25
-
-
0028883794
-
Determination of the conformation of folding initiation sites in proteins by computer simulation
-
Avbelj F, Moult J (1995) Determination of the conformation of folding initiation sites in proteins by computer simulation. Proteins 23: 129-141.
-
(1995)
Proteins
, vol.23
, pp. 129-141
-
-
Avbelj, F.1
Moult, J.2
-
26
-
-
0029055313
-
LINUS: A hierarchic procedure to predict the fold of a protein
-
Srinivasan R, Rose GD (1995) LINUS: A hierarchic procedure to predict the fold of a protein. Proteins 22: 81-99.
-
(1995)
Proteins
, vol.22
, pp. 81-99
-
-
Srinivasan, R.1
Rose, G.D.2
-
27
-
-
0035342435
-
Ab initio protein structure prediction using physicochemical potentials and a simplified off-lattice model
-
Gibbs N, Clarke AR, Sessions RB (2001) Ab initio protein structure prediction using physicochemical potentials and a simplified off-lattice model. Proteins 43: 186-202.
-
(2001)
Proteins
, vol.43
, pp. 186-202
-
-
Gibbs, N.1
Clarke, A.R.2
Sessions, R.B.3
-
28
-
-
0037196323
-
Ab initio prediction of helical segments in polypeptides
-
Klepeis JL, Floudas CA (2002) Ab initio prediction of helical segments in polypeptides. J Comput Chem 23: 245-266.
-
(2002)
J Comput Chem
, vol.23
, pp. 245-266
-
-
Klepeis, J.L.1
Floudas, C.A.2
-
29
-
-
0033557181
-
Folding-unfolding thermodynamics of a beta-heptapeptide from equilibrium simulations
-
Daura X, van Gunsteren WF, Mark AE (1999) Folding-unfolding thermodynamics of a beta-heptapeptide from equilibrium simulations. Proteins 34: 269-280.
-
(1999)
Proteins
, vol.34
, pp. 269-280
-
-
Daura, X.1
Van Gunsteren, W.F.2
Mark, A.E.3
-
30
-
-
0035946983
-
Essential dynamics of reversible peptide folding: Memory-free conformational dynamics governed by internal hydrogen bonds
-
de Groot BL, Daura X, Mark AE, Grubmuller H (2001) Essential dynamics of reversible peptide folding: Memory-free conformational dynamics governed by internal hydrogen bonds. J Mol Biol 309: 299-313.
-
(2001)
J Mol Biol
, vol.309
, pp. 299-313
-
-
De Groot, B.L.1
Daura, X.2
Mark, A.E.3
Grubmuller, H.4
-
31
-
-
10844292652
-
Energy landscape of a small peptide revealed by dihedral angle principal component analysis
-
Mu Y, Nguyen PH, Stock G (2005) Energy landscape of a small peptide revealed by dihedral angle principal component analysis. Proteins 58: 45-52.
-
(2005)
Proteins
, vol.58
, pp. 45-52
-
-
Mu, Y.1
Nguyen, P.H.2
Stock, G.3
-
32
-
-
0037339393
-
Helix propensities of short peptides: Molecular dynamics versus bioinformatics
-
Bystroff C, Garde S (2003) Helix propensities of short peptides: Molecular dynamics versus bioinformatics. Proteins 50: 552-562.
-
(2003)
Proteins
, vol.50
, pp. 552-562
-
-
Bystroff, C.1
Garde, S.2
-
33
-
-
0020024242
-
Specific intermediates in the folding reactions of small proteins and the mechanism of protein folding
-
Kim PS, Baldwin RL (1982) Specific intermediates in the folding reactions of small proteins and the mechanism of protein folding. Annu Rev Biochem 51: 459-489.
-
(1982)
Annu Rev Biochem
, vol.51
, pp. 459-489
-
-
Kim, P.S.1
Baldwin, R.L.2
-
34
-
-
0027405357
-
Cooperativity in protein-folding kinetics
-
U S A
-
Dill KA, Fiebig KM, Chan HS (1993) Cooperativity in protein-folding kinetics. Proc Natl Acad Sci U S A 90: 1942-1946.
-
(1993)
Proc Natl Acad Sci
, vol.90
, pp. 1942-1946
-
-
Dill, K.A.1
Fiebig, K.M.2
Chan, H.S.3
-
35
-
-
0032972986
-
Is protein folding hierarchic? I. Local structure and peptide folding
-
Baldwin RL, Rose GD (1999) Is protein folding hierarchic? I. Local structure and peptide folding. Trends Biochem Sci 24: 26-33.
-
(1999)
Trends Biochem Sci
, vol.24
, pp. 26-33
-
-
Baldwin, R.L.1
Rose, G.D.2
-
36
-
-
0001616080
-
Replica-exchange molecular dynamics method for protein folding
-
Sugita Y, Okamoto Y (1999) Replica-exchange molecular dynamics method for protein folding. Chemical Physics Letters 314: 141-151.
-
(1999)
Chemical Physics Letters
, vol.314
, pp. 141-151
-
-
Sugita, Y.1
Okamoto, Y.2
-
37
-
-
14244273182
-
Theory and applications of the generalized Born solvation model in macromolecular simulations
-
Tsui V, Case DA (2000) Theory and applications of the generalized Born solvation model in macromolecular simulations. Biopolymers 56: 275-291.
-
(2000)
Biopolymers
, vol.56
, pp. 275-291
-
-
Tsui, V.1
Case, D.A.2
-
38
-
-
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
-
39
-
-
0029865623
-
Context-dependent secondary structure formation of a designed protein sequence
-
Minor DL Jr, Kim PS (1996) Context-dependent secondary structure formation of a designed protein sequence. Nature 380: 730-734.
-
(1996)
Nature
, vol.380
, pp. 730-734
-
-
Minor Jr., D.L.1
Kim, P.S.2
-
40
-
-
0028226386
-
Bai Y, Englander SW (1994) Hydrogen bond strength and beta-sheet propensities: The role of a side chain blocking effect
-
Bai Y, Englander SW (1994) . Bai Y, Englander SW (1994) Hydrogen bond strength and beta-sheet propensities: The role of a side chain blocking effect. Proteins 18, 262-266.
-
(1994)
Proteins
, vol.18
, pp. 262-266
-
-
Bai, Y.1
Englander, S.W.2
-
41
-
-
0027749370
-
Formation of a molten globule intermediate early in the kinetic folding pathway of apomyoglobin
-
Jennings PA, Wright PE (1993) Formation of a molten globule intermediate early in the kinetic folding pathway of apomyoglobin. Science 262: 892-896.
-
(1993)
Science
, vol.262
, pp. 892-896
-
-
Jennings, P.A.1
Wright, P.E.2
-
42
-
-
0028848469
-
Search for nucleation sites in smaller fragments of chymotrypsin inhibitor 2
-
Itzhaki LS, Neira JL, Ruiz-Sanz J, de Prat Gay G, Fersht AR (1995) Search for nucleation sites in smaller fragments of chymotrypsin inhibitor 2. J Mol Biol 254: 289-304.
-
(1995)
J Mol Biol
, vol.254
, pp. 289-304
-
-
Itzhaki, L.S.1
Neira, J.L.2
Ruiz-Sanz, J.3
De Prat Gay, G.4
Fersht, A.R.5
-
43
-
-
0343059020
-
Conformational analysis of peptides corresponding to beta-hairpins and a beta-sheet that represent the entire sequence of the alpha-spectrin SH3 domain
-
Viguera AR, Jimenez MA, Rico M, Serrano L (1996) Conformational analysis of peptides corresponding to beta-hairpins and a beta-sheet that represent the entire sequence of the alpha-spectrin SH3 domain. J Mol Biol 255: 507-521.
-
(1996)
J Mol Biol
, vol.255
, pp. 507-521
-
-
Viguera, A.R.1
Jimenez, M.A.2
Rico, M.3
Serrano, L.4
-
44
-
-
0024413264
-
Water-inserted alpha-helical segments implicate reverse turns as folding intermediates
-
Sundaralingam M, Sekharudu YC (1989) Water-inserted alpha-helical segments implicate reverse turns as folding intermediates. Science 244: 1333-1337.
-
(1989)
Science
, vol.244
, pp. 1333-1337
-
-
Sundaralingam, M.1
Sekharudu, Y.C.2
-
45
-
-
0026237127
-
Unfolding of an alpha-helix in water
-
Soman KV, Karimi A, Case DA (1991) Unfolding of an alpha-helix in water. Biopolymers 31: 1351-1361.
-
(1991)
Biopolymers
, vol.31
, pp. 1351-1361
-
-
Soman, K.V.1
Karimi, A.2
Case, D.A.3
-
46
-
-
8644237364
-
Understanding the key factors that control the rate of beta-hairpin folding
-
U S A
-
Du D, Zhu Y, Huang CY, Gai F (2004) Understanding the key factors that control the rate of beta-hairpin folding. Proc Natl Acad Sci U S A 101: 15915-15920.
-
(2004)
Proc Natl Acad Sci
, vol.101
, pp. 15915-15920
-
-
Du, D.1
Zhu, Y.2
Huang, C.Y.3
Gai, F.4
-
47
-
-
0034646218
-
Mechanisms and kinetics of beta-hairpin formation
-
U S A
-
Klimov DK, Thirumalai D (2000) Mechanisms and kinetics of beta-hairpin formation. Proc Natl Acad Sci U S A 97: 2544-2549.
-
(2000)
Proc Natl Acad Sci
, vol.97
, pp. 2544-2549
-
-
Klimov, D.K.1
Thirumalai, D.2
-
48
-
-
0038502170
-
Folding dynamics and mechanism of beta-hairpin formation
-
Munoz V, Thompson PA, Hofrichter J, Eaton WA (1997) Folding dynamics and mechanism of beta-hairpin formation. Nature 390: 196-199.
-
(1997)
Nature
, vol.390
, pp. 196-199
-
-
Munoz, V.1
Thompson, P.A.2
Hofrichter, J.3
Eaton, W.A.4
-
49
-
-
0029633186
-
Amber, a package of computer-programs for applying molecular mechanics, normal-mode analysis, molecular-dynamics and free-energy calculations to simulate the structural and energetic properties of molecules
-
Pearlman DA, Case DA, Caldwell JW, Ross WS, Cheatham TE, et al. (1995) Amber, a package of computer-programs for applying molecular mechanics, normal-mode analysis, molecular-dynamics and free-energy calculations to simulate the structural and energetic properties of molecules. Comput Physics Commun 91: 1-41.
-
(1995)
Comput Physics Commun
, vol.91
, pp. 1-41
-
-
Pearlman, D.A.1
Case, D.A.2
Caldwell, J.W.3
Ross, W.S.4
Cheatham, T.E.5
-
50
-
-
33646940952
-
Numerical-integration of Cartesian equations of motion of a system with constraints - Molecular-dynamics of N-alkanes
-
Ryckaert JP, Ciccotti G, Berendsen HJC (1977) Numerical-integration of Cartesian equations of motion of a system with constraints - molecular-dynamics of N-alkanes. Journal of Computational Physics 23: 327-341.
-
(1977)
Journal of Computational Physics
, vol.23
, pp. 327-341
-
-
Ryckaert, J.P.1
Ciccotti, G.2
Berendsen, H.J.C.3
-
51
-
-
33947398571
-
Use of the Weighted Histogram Analysis Method for the analysis of simulated and parallel tempering simulations
-
In press
-
Chodera JD, Swope WC, Pitera JW, Seok C, Dill KA (2006) Use of the Weighted Histogram Analysis Method for the analysis of simulated and parallel tempering simulations. J Chem Theory Comput: In press.
-
(2006)
J Chem Theory Comput
-
-
Chodera, J.D.1
Swope, W.C.2
Pitera, J.W.3
Seok, C.4
Dill, K.A.5
-
52
-
-
84986519238
-
The Weighted Histogram Analysis Method for free-energy calculations on biomolecules. 1. The method
-
Kumar S, Bouzida D, Swendsen RH, Kollman PA, Rosenberg JM (1992) The Weighted Histogram Analysis Method for free-energy calculations on biomolecules. 1. The method. J Comput Chem 13: 1011-1021.
-
(1992)
J Comput Chem
, vol.13
, pp. 1011-1021
-
-
Kumar, S.1
Bouzida, D.2
Swendsen, R.H.3
Kollman, P.A.4
Rosenberg, J.M.5
-
54
-
-
0030010605
-
Experimentally observed conformation-dependent geometry and hidden strain in proteins
-
Karplus PA (1996) Experimentally observed conformation-dependent geometry and hidden strain in proteins. Protein Sci 5: 1406-1420.
-
(1996)
Protein Sci
, vol.5
, pp. 1406-1420
-
-
Karplus, P.A.1
-
55
-
-
0142179047
-
Revisiting the Ramachandran plot: Hard-sphere repulsion, electrostatics, and H-bonding in the alpha-helix
-
Ho BK, Thomas A, Brasseur R (2003) Revisiting the Ramachandran plot: Hard-sphere repulsion, electrostatics, and H-bonding in the alpha-helix. Protein Sci 12: 2508-2522.
-
(2003)
Protein Sci
, vol.12
, pp. 2508-2522
-
-
Ho, B.K.1
Thomas, A.2
Brasseur, R.3
|