-
1
-
-
0015967881
-
Conformational parameters for amino acids in helical, beta-sheet, and random coil regions calculated from proteins
-
Chou P.Y., and Fasman G.D. Conformational parameters for amino acids in helical, beta-sheet, and random coil regions calculated from proteins. Biochemistry 13 (1974) 211-222
-
(1974)
Biochemistry
, vol.13
, pp. 211-222
-
-
Chou, P.Y.1
Fasman, G.D.2
-
2
-
-
0028158628
-
PHD-an automatic mail server for protein secondary structure prediction
-
Rost B., Sander C., and Schneider R. PHD-an automatic mail server for protein secondary structure prediction. Comput. Appl. Biosci. 10 (1994) 53-60
-
(1994)
Comput. Appl. Biosci.
, vol.10
, pp. 53-60
-
-
Rost, B.1
Sander, C.2
Schneider, R.3
-
3
-
-
0033106244
-
Evaluation and improvement of multiple sequence methods for protein secondary structure prediction
-
Cuff J.A., and Barton G.J. Evaluation and improvement of multiple sequence methods for protein secondary structure prediction. Proteins: Struct. Funct. Genet. 34 (1999) 508-519
-
(1999)
Proteins: Struct. Funct. Genet.
, vol.34
, pp. 508-519
-
-
Cuff, J.A.1
Barton, G.J.2
-
4
-
-
0028568650
-
Intrinsic secondary structure propensities of the amino acids, using statistical phi-psi matrices: comparison with experimental scales
-
Munoz V., and Serrano L. Intrinsic secondary structure propensities of the amino acids, using statistical phi-psi matrices: comparison with experimental scales. Proteins: Struct. Funct. Genet. 20 (1994) 301-311
-
(1994)
Proteins: Struct. Funct. Genet.
, vol.20
, pp. 301-311
-
-
Munoz, V.1
Serrano, L.2
-
5
-
-
0028176595
-
Measurement of the beta-sheet-forming propensities of amino acids
-
Minor Jr. D.L., and Kim P.S. Measurement of the beta-sheet-forming propensities of amino acids. Nature 367 (1994) 660-663
-
(1994)
Nature
, vol.367
, pp. 660-663
-
-
Minor Jr., D.L.1
Kim, P.S.2
-
6
-
-
0027411181
-
Thermodynamic beta-sheet propensities measured using a zinc-finger host peptide
-
Kim C.A., and Berg J.M. Thermodynamic beta-sheet propensities measured using a zinc-finger host peptide. Nature 362 (1993) 267-270
-
(1993)
Nature
, vol.362
, pp. 267-270
-
-
Kim, C.A.1
Berg, J.M.2
-
7
-
-
0028175780
-
A thermodynamic scale for the beta-sheet forming tendencies of the amino acids
-
Smith C.K., Withka J.M., and Regan L. A thermodynamic scale for the beta-sheet forming tendencies of the amino acids. Biochemistry 33 (1994) 5510-5517
-
(1994)
Biochemistry
, vol.33
, pp. 5510-5517
-
-
Smith, C.K.1
Withka, J.M.2
Regan, L.3
-
8
-
-
0025222978
-
A thermodynamic scale for the helix-forming tendencies of the commonly occurring amino acids
-
O'Neil K.T., and DeGrado W.F. A thermodynamic scale for the helix-forming tendencies of the commonly occurring amino acids. Science 250 (1990) 646-651
-
(1990)
Science
, vol.250
, pp. 646-651
-
-
O'Neil, K.T.1
DeGrado, W.F.2
-
9
-
-
0025253106
-
Relative helix-forming tendencies of nonpolar amino acids
-
Padmanabhan S., Marqusee S., Ridgeway T., Laue T. M., and Baldwin R.L. Relative helix-forming tendencies of nonpolar amino acids. Nature 344 (1990) 268-270
-
(1990)
Nature
, vol.344
, pp. 268-270
-
-
Padmanabhan, S.1
Marqusee, S.2
Ridgeway, T.3
Laue, T. M.4
Baldwin, R.L.5
-
10
-
-
0028988836
-
Side-chain determinants of beta-sheet stability
-
Otzen D.E., and Fersht A.R. Side-chain determinants of beta-sheet stability. Biochemistry 34 (1995) 5718-5724
-
(1995)
Biochemistry
, vol.34
, pp. 5718-5724
-
-
Otzen, D.E.1
Fersht, A.R.2
-
11
-
-
0027998757
-
Context is a major determinant of beta-sheet propensity
-
Minor Jr. D.L., and Kim P.S. Context is a major determinant of beta-sheet propensity. Nature 371 (1994) 264-267
-
(1994)
Nature
, vol.371
, pp. 264-267
-
-
Minor Jr., D.L.1
Kim, P.S.2
-
12
-
-
0028792105
-
Guidelines for protein design: the energetics of beta sheet side chain interactions
-
Smith C.K., and Regan L. Guidelines for protein design: the energetics of beta sheet side chain interactions. Science 270 (1995) 980-982
-
(1995)
Science
, vol.270
, pp. 980-982
-
-
Smith, C.K.1
Regan, L.2
-
13
-
-
0032815297
-
Context-dependence of amino acid residue pairing in antiparallel beta-sheets
-
Zaremba S.M., and Gregoret L.M. Context-dependence of amino acid residue pairing in antiparallel beta-sheets. J. Mol. Biol. 291 (1999) 463-479
-
(1999)
J. Mol. Biol.
, vol.291
, pp. 463-479
-
-
Zaremba, S.M.1
Gregoret, L.M.2
-
14
-
-
14844320178
-
The protein folding transition state: what are Phi-values really telling us?
-
Raleigh D.P., and Plaxco K.W. The protein folding transition state: what are Phi-values really telling us?. Protein Pept. Letters 12 (2005) 117-122
-
(2005)
Protein Pept. Letters
, vol.12
, pp. 117-122
-
-
Raleigh, D.P.1
Plaxco, K.W.2
-
15
-
-
13844299144
-
The family feud: do proteins with similar structures fold via the same pathway?
-
Zarrine-Afsar A., Larson S.M., and Davidson A.R. The family feud: do proteins with similar structures fold via the same pathway?. Curr. Opin. Struct. Biol. 15 (2005) 42-49
-
(2005)
Curr. Opin. Struct. Biol.
, vol.15
, pp. 42-49
-
-
Zarrine-Afsar, A.1
Larson, S.M.2
Davidson, A.R.3
-
16
-
-
0037221599
-
Is there a unifying mechanism for protein folding?
-
Daggett V., and Fersht A.R. Is there a unifying mechanism for protein folding?. Trends Biochem. Sci. 28 (2003) 18-25
-
(2003)
Trends Biochem. Sci.
, vol.28
, pp. 18-25
-
-
Daggett, V.1
Fersht, A.R.2
-
17
-
-
0024358426
-
Mapping the transition state and pathway of protein folding by protein engineering
-
Matouschek A., Kellis Jr. J.T., Serrano L., and Fersht A.R. Mapping the transition state and pathway of protein folding by protein engineering. Nature 340 (1989) 122-126
-
(1989)
Nature
, vol.340
, pp. 122-126
-
-
Matouschek, A.1
Kellis Jr., J.T.2
Serrano, L.3
Fersht, A.R.4
-
18
-
-
0026354152
-
Protein engineering in analysis of protein folding pathways and stability
-
Matouschek A., and Fersht A.R. Protein engineering in analysis of protein folding pathways and stability. Methods Enzymol. 202 (1991) 82-112
-
(1991)
Methods Enzymol.
, vol.202
, pp. 82-112
-
-
Matouschek, A.1
Fersht, A.R.2
-
19
-
-
0032750509
-
The folding transition state between SH3 domains is conformationally restricted and evolutionarily conserved
-
Martinez J.C., and Serrano L. The folding transition state between SH3 domains is conformationally restricted and evolutionarily conserved. Nature Struct. Biol. 6 (1999) 1010-1016
-
(1999)
Nature Struct. Biol.
, vol.6
, pp. 1010-1016
-
-
Martinez, J.C.1
Serrano, L.2
-
20
-
-
0036172116
-
Hydrophobic core packing in the SH3 domain folding transition state
-
Northey J.G., Di Nardo A.A., and Davidson A.R. Hydrophobic core packing in the SH3 domain folding transition state. Nature Struct. Biol. 9 (2002) 126-130
-
(2002)
Nature Struct. Biol.
, vol.9
, pp. 126-130
-
-
Northey, J.G.1
Di Nardo, A.A.2
Davidson, A.R.3
-
21
-
-
0036296248
-
Protein folding kinetics beyond the phi value: using multiple amino acid substitutions to investigate the structure of the SH3 domain folding transition state
-
Northey J.G., Maxwell K.L., and Davidson A.R. Protein folding kinetics beyond the phi value: using multiple amino acid substitutions to investigate the structure of the SH3 domain folding transition state. J. Mol. Biol. 320 (2002) 389-402
-
(2002)
J. Mol. Biol.
, vol.320
, pp. 389-402
-
-
Northey, J.G.1
Maxwell, K.L.2
Davidson, A.R.3
-
23
-
-
0032734515
-
Experiment and theory highlight role of native state topology in SH3 folding
-
Riddle D.S., Grantcharova V.P., Santiago J.V., Alm E., Ruczinski I., and Baker D. Experiment and theory highlight role of native state topology in SH3 folding. Nature Struct. Biol. 6 (1999) 1016-1024
-
(1999)
Nature Struct. Biol.
, vol.6
, pp. 1016-1024
-
-
Riddle, D.S.1
Grantcharova, V.P.2
Santiago, J.V.3
Alm, E.4
Ruczinski, I.5
Baker, D.6
-
24
-
-
0035970299
-
Dramatic stabilization of an SH3 domain by a single substitution: roles of the folded and unfolded states
-
Mok Y.K., Elisseeva E.L., Davidson A.R., and Forman-Kay J.D. Dramatic stabilization of an SH3 domain by a single substitution: roles of the folded and unfolded states. J. Mol. Biol. 307 (2001) 913-928
-
(2001)
J. Mol. Biol.
, vol.307
, pp. 913-928
-
-
Mok, Y.K.1
Elisseeva, E.L.2
Davidson, A.R.3
Forman-Kay, J.D.4
-
25
-
-
27744452242
-
Fine structure analysis of a protein folding transition state; distinguishing between hydrophobic stabilization and specific packing
-
Anil B., Sato S., Cho J.H., and Raleigh D.P. Fine structure analysis of a protein folding transition state; distinguishing between hydrophobic stabilization and specific packing. J. Mol. Biol. 354 (2005) 693-705
-
(2005)
J. Mol. Biol.
, vol.354
, pp. 693-705
-
-
Anil, B.1
Sato, S.2
Cho, J.H.3
Raleigh, D.P.4
-
26
-
-
9644264177
-
Context-dependent effects of proline residues on the stability and folding pathway of ubiquitin
-
Crespo M.D., Platt G.W., Bofill R., and Searle M.S. Context-dependent effects of proline residues on the stability and folding pathway of ubiquitin. Eur. J. Biochem. 271 (2004) 4474-4484
-
(2004)
Eur. J. Biochem.
, vol.271
, pp. 4474-4484
-
-
Crespo, M.D.1
Platt, G.W.2
Bofill, R.3
Searle, M.S.4
-
27
-
-
33645537945
-
Engineering diverse changes in beta-turn propensities in the N-terminal beta-hairpin of ubiquitin reveals significant effects on stability and kinetics but a robust folding transition state
-
Simpson E.R., Meldrum J.K., and Searle M.S. Engineering diverse changes in beta-turn propensities in the N-terminal beta-hairpin of ubiquitin reveals significant effects on stability and kinetics but a robust folding transition state. Biochemistry 45 (2006) 4220-4230
-
(2006)
Biochemistry
, vol.45
, pp. 4220-4230
-
-
Simpson, E.R.1
Meldrum, J.K.2
Searle, M.S.3
-
28
-
-
0028037217
-
Single versus parallel pathways of protein folding and fractional formation of structure in the transition state
-
Fersht A.R., Itzhaki L.S., elMasry N.F., Matthews J.M., and Otzen D.E. Single versus parallel pathways of protein folding and fractional formation of structure in the transition state. Proc. Natl Acad. Sci. USA 91 (1994) 10426-10429
-
(1994)
Proc. Natl Acad. Sci. USA
, vol.91
, pp. 10426-10429
-
-
Fersht, A.R.1
Itzhaki, L.S.2
elMasry, N.F.3
Matthews, J.M.4
Otzen, D.E.5
-
29
-
-
0029865623
-
Context-dependent secondary structure formation of a designed protein sequence
-
Minor Jr. D.L., and Kim P.S. Context-dependent secondary structure formation of a designed protein sequence. Nature 380 (1996) 730-734
-
(1996)
Nature
, vol.380
, pp. 730-734
-
-
Minor Jr., D.L.1
Kim, P.S.2
-
30
-
-
0033604845
-
Effects of core mutations on the folding of a beta-sheet protein: implications for backbone organization in the I-state
-
Lorch M., Mason J.M., Clarke A.R., and Parker M.J. Effects of core mutations on the folding of a beta-sheet protein: implications for backbone organization in the I-state. Biochemistry 38 (1999) 1377-1385
-
(1999)
Biochemistry
, vol.38
, pp. 1377-1385
-
-
Lorch, M.1
Mason, J.M.2
Clarke, A.R.3
Parker, M.J.4
-
31
-
-
2542619154
-
Dramatic acceleration of protein folding by stabilization of a nonnative backbone conformation
-
Di Nardo A.A., Korzhnev D.M., Stogios P.J., Zarrine-Afsar A., Kay L.E., and Davidson A.R. Dramatic acceleration of protein folding by stabilization of a nonnative backbone conformation. Proc. Natl Acad. Sci. USA 101 (2004) 7954-7959
-
(2004)
Proc. Natl Acad. Sci. USA
, vol.101
, pp. 7954-7959
-
-
Di Nardo, A.A.1
Korzhnev, D.M.2
Stogios, P.J.3
Zarrine-Afsar, A.4
Kay, L.E.5
Davidson, A.R.6
-
32
-
-
0036266942
-
Conformational strain in the hydrophobic core and its implications for protein folding and design
-
Ventura S., Vega M.C., Lacroix E., Angrand I., Spagnolo L., and Serrano L. Conformational strain in the hydrophobic core and its implications for protein folding and design. Nature Struct. Biol. 9 (2002) 485-493
-
(2002)
Nature Struct. Biol.
, vol.9
, pp. 485-493
-
-
Ventura, S.1
Vega, M.C.2
Lacroix, E.3
Angrand, I.4
Spagnolo, L.5
Serrano, L.6
-
33
-
-
0037117477
-
Unspecific hydrophobic stabilization of folding transition states
-
Viguera A.R., Vega C., and Serrano L. Unspecific hydrophobic stabilization of folding transition states. Proc. Natl Acad. Sci. USA 99 (2002) 5349-5354
-
(2002)
Proc. Natl Acad. Sci. USA
, vol.99
, pp. 5349-5354
-
-
Viguera, A.R.1
Vega, C.2
Serrano, L.3
-
34
-
-
0020997912
-
Dictionary of protein secondary structure - pattern-recognition of hydrogen-bonded and geometrical features
-
Kabsch W., and Sander C. Dictionary of protein secondary structure - pattern-recognition of hydrogen-bonded and geometrical features. Biopolymers 22 (1983) 2577-2637
-
(1983)
Biopolymers
, vol.22
, pp. 2577-2637
-
-
Kabsch, W.1
Sander, C.2
-
35
-
-
33646853740
-
The protein data bank (PDB) as a versatile resource for glycobiology and glycomics
-
Lutteke T., and Von der Lieth C.W. The protein data bank (PDB) as a versatile resource for glycobiology and glycomics. Biocatal. Biotransform. 24 (2006) 147-155
-
(2006)
Biocatal. Biotransform.
, vol.24
, pp. 147-155
-
-
Lutteke, T.1
Von der Lieth, C.W.2
-
36
-
-
0034113648
-
beta-sheet propensity and its correlation with parameters based on conformation
-
Pal D., and Chakrabarti P. beta-sheet propensity and its correlation with parameters based on conformation. Acta Crystallog. sect. D 56 (2000) 589-594
-
(2000)
Acta Crystallog. sect. D
, vol.56
, pp. 589-594
-
-
Pal, D.1
Chakrabarti, P.2
-
37
-
-
0029147823
-
Intrinsic phi, psi propensities of amino acids, derived from the coil regions of known structures
-
Swindells M.B., MacArthur M.W., and Thornton J.M. Intrinsic phi, psi propensities of amino acids, derived from the coil regions of known structures. Nature Struct. Biol. 2 (1995) 596-603
-
(1995)
Nature Struct. Biol.
, vol.2
, pp. 596-603
-
-
Swindells, M.B.1
MacArthur, M.W.2
Thornton, J.M.3
-
38
-
-
0027171034
-
Application of physical organic chemistry to engineered mutants of proteins: Hammond postulate behavior in the transition state of protein folding
-
Matouschek A., and Fersht A.R. Application of physical organic chemistry to engineered mutants of proteins: Hammond postulate behavior in the transition state of protein folding. Proc. Natl Acad. Sci. USA 90 (1993) 7814-7818
-
(1993)
Proc. Natl Acad. Sci. USA
, vol.90
, pp. 7814-7818
-
-
Matouschek, A.1
Fersht, A.R.2
-
39
-
-
0037418635
-
Hammond behavior versus ground state effects in protein folding: evidence for narrow free energy barriers and residual structure in unfolded states
-
Sanchez I.E., and Kiefhaber T. Hammond behavior versus ground state effects in protein folding: evidence for narrow free energy barriers and residual structure in unfolded states. J. Mol. Biol. 327 (2003) 867-884
-
(2003)
J. Mol. Biol.
, vol.327
, pp. 867-884
-
-
Sanchez, I.E.1
Kiefhaber, T.2
-
40
-
-
0029859858
-
Surface point mutations that significantly alter the structure and stability of a protein's denatured state
-
Smith C.K., Bu Z., Anderson K.S., Sturtevant J.M., Engelman D.M., and Regan L. Surface point mutations that significantly alter the structure and stability of a protein's denatured state. Protein Sci. 5 (1996) 2009-2019
-
(1996)
Protein Sci.
, vol.5
, pp. 2009-2019
-
-
Smith, C.K.1
Bu, Z.2
Anderson, K.S.3
Sturtevant, J.M.4
Engelman, D.M.5
Regan, L.6
-
41
-
-
0031588693
-
Folding kinetics of Che Y mutants with enhanced native alpha-helix propensities
-
Lopez-Hernandez E., Cronet P., Serrano L., and Munoz V. Folding kinetics of Che Y mutants with enhanced native alpha-helix propensities. J. Mol. Biol. 266 (1997) 610-620
-
(1997)
J. Mol. Biol.
, vol.266
, pp. 610-620
-
-
Lopez-Hernandez, E.1
Cronet, P.2
Serrano, L.3
Munoz, V.4
-
42
-
-
33846026304
-
Transition-states in protein folding kinetics: the structural interpretation of phi values
-
Weikl T.R., and Dill K.A. Transition-states in protein folding kinetics: the structural interpretation of phi values. J. Mol. Biol. 365 (2007) 1578-1586
-
(2007)
J. Mol. Biol.
, vol.365
, pp. 1578-1586
-
-
Weikl, T.R.1
Dill, K.A.2
-
43
-
-
0032542018
-
Mutagenesis of a buried polar interaction in an SH3 domain: sequence conservation provides the best prediction of stability effects
-
Maxwell K.L., and Davidson A.R. Mutagenesis of a buried polar interaction in an SH3 domain: sequence conservation provides the best prediction of stability effects. Biochemistry 37 (1998) 16172-16182
-
(1998)
Biochemistry
, vol.37
, pp. 16172-16182
-
-
Maxwell, K.L.1
Davidson, A.R.2
-
44
-
-
0028871804
-
How to measure and predict the molar absorption coefficient of a protein
-
Pace C.N., Vajdos F., Fee L., Grimsley G., and Gray T. How to measure and predict the molar absorption coefficient of a protein. Protein Sci. 4 (1995) 2411-2423
-
(1995)
Protein Sci.
, vol.4
, pp. 2411-2423
-
-
Pace, C.N.1
Vajdos, F.2
Fee, L.3
Grimsley, G.4
Gray, T.5
-
45
-
-
0031808274
-
Baseline length and automated fitting of denaturation data
-
Allen D.L., and Pielak G.J. Baseline length and automated fitting of denaturation data. Protein Sci. 7 (1998) 1262-1263
-
(1998)
Protein Sci.
, vol.7
, pp. 1262-1263
-
-
Allen, D.L.1
Pielak, G.J.2
-
46
-
-
0000484499
-
Hydrophobic parameters-pi of amino-acid side-chains from the partitioning of n-acetyl-amino-acid amides
-
Fauchere J.L., and Pliska V. Hydrophobic parameters-pi of amino-acid side-chains from the partitioning of n-acetyl-amino-acid amides. Eur. J. Med. Chem. 18 (1983) 369-375
-
(1983)
Eur. J. Med. Chem.
, vol.18
, pp. 369-375
-
-
Fauchere, J.L.1
Pliska, V.2
|