-
1
-
-
0023449962
-
Spin glasses and the statistical mechanics of protein folding
-
J.D. Bryngelson, and P.G. Wolynes Spin glasses and the statistical mechanics of protein folding Proc. Natl Acad. Sci. USA 84 1987 7524 7528
-
(1987)
Proc. Natl Acad. Sci. USA
, vol.84
, pp. 7524-7528
-
-
Bryngelson, J.D.1
Wolynes, P.G.2
-
2
-
-
0034685604
-
Topological and energetic factors: What determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins
-
C. Clementi, H. Nymeyer, and J.N. Onuchic Topological and energetic factors: what determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins J. Mol. Biol. 298 2000 937 953
-
(2000)
J. Mol. Biol.
, vol.298
, pp. 937-953
-
-
Clementi, C.1
Nymeyer, H.2
Onuchic, J.N.3
-
4
-
-
0034604105
-
A surprising simplicity to protein folding
-
D. Baker A surprising simplicity to protein folding Nature 405 2000 39 42
-
(2000)
Nature
, vol.405
, pp. 39-42
-
-
Baker, D.1
-
5
-
-
0035850732
-
Roles of native topology and chain-length scaling in protein folding: A simulation study with a Go-like model
-
N. Koga, and S. Takada Roles of native topology and chain-length scaling in protein folding: a simulation study with a Go-like model J. Mol. Biol. 313 2001 171 180
-
(2001)
J. Mol. Biol.
, vol.313
, pp. 171-180
-
-
Koga, N.1
Takada, S.2
-
6
-
-
0034705115
-
How native-state topology affects the folding of dihydrofolate reductase and interleukin-1beta
-
C. Clementi, P.A. Jennings, and J.N. Onuchic How native-state topology affects the folding of dihydrofolate reductase and interleukin-1beta Proc. Natl Acad. Sci. USA 97 2000 5871 5876
-
(2000)
Proc. Natl Acad. Sci. USA
, vol.97
, pp. 5871-5876
-
-
Clementi, C.1
Jennings, P.A.2
Onuchic, J.N.3
-
7
-
-
0037459022
-
Interplay among tertiary contacts, secondary structure formation and side-chain packing in the protein folding mechanism: All-atom representation study of protein L
-
C. Clementi, A.E. Garcia, and J.N. Onuchic Interplay among tertiary contacts, secondary structure formation and side-chain packing in the protein folding mechanism: all-atom representation study of protein L J. Mol. Biol. 326 2003 933 954
-
(2003)
J. Mol. Biol.
, vol.326
, pp. 933-954
-
-
Clementi, C.1
Garcia, A.E.2
Onuchic, J.N.3
-
8
-
-
0041428117
-
The folding and design of repeat proteins: Reaching a consensus
-
E.R. Main, S.E. Jackson, and L. Regan The folding and design of repeat proteins: reaching a consensus Curr. Opin. Struct. Biol. 13 2003 482 489
-
(2003)
Curr. Opin. Struct. Biol.
, vol.13
, pp. 482-489
-
-
Main, E.R.1
Jackson, S.E.2
Regan, L.3
-
9
-
-
0032792551
-
The ankyrin repeat: A diversity of interactions on a common structural framework
-
S.G. Sedgwick, and S.J. Smerdon The ankyrin repeat: a diversity of interactions on a common structural framework Trends Biochem. Sci. 24 1999 311 316
-
(1999)
Trends Biochem. Sci.
, vol.24
, pp. 311-316
-
-
Sedgwick, S.G.1
Smerdon, S.J.2
-
10
-
-
0027333330
-
Hundreds of ankyrin-like repeats in functionally diverse proteins: Mobile modules that cross phyla horizontally?
-
P. Bork Hundreds of ankyrin-like repeats in functionally diverse proteins: mobile modules that cross phyla horizontally? Proteins: Struct. Funct. Genet. 17 1993 363 374
-
(1993)
Proteins: Struct. Funct. Genet.
, vol.17
, pp. 363-374
-
-
Bork, P.1
-
11
-
-
0023280623
-
Similarity between cell-cycle genes of budding yeast and fission yeast and the Notch gene of Drosophila
-
L. Breeden, and K. Nasmyth Similarity between cell-cycle genes of budding yeast and fission yeast and the Notch gene of Drosophila Nature 329 1987 651 654
-
(1987)
Nature
, vol.329
, pp. 651-654
-
-
Breeden, L.1
Nasmyth, K.2
-
12
-
-
0027374511
-
The membrane-binding domain of ankyrin contains four independently folded subdomains, each comprised of six ankyrin repeats
-
P. Michaely, and V. Bennett The membrane-binding domain of ankyrin contains four independently folded subdomains, each comprised of six ankyrin repeats J. Biol. Chem. 268 1993 22703 22709
-
(1993)
J. Biol. Chem.
, vol.268
, pp. 22703-22709
-
-
Michaely, P.1
Bennett, V.2
-
13
-
-
0345864022
-
SMART 4.0: Towards genomic data integration
-
I. Letunic, R.R. Copley, S. Schmidt, F.D. Ciccarelli, T. Doerks, and J. Schultz SMART 4.0: towards genomic data integration Nucl. Acids Res. 32 2004 D142 D144
-
(2004)
Nucl. Acids Res.
, vol.32
-
-
Letunic, I.1
Copley, R.R.2
Schmidt, S.3
Ciccarelli, F.D.4
Doerks, T.5
Schultz, J.6
-
14
-
-
0033150672
-
Topological characteristics of helical repeat proteins
-
M.R. Groves, and D. Barford Topological characteristics of helical repeat proteins Curr. Opin. Struct. Biol. 9 1999 383 389
-
(1999)
Curr. Opin. Struct. Biol.
, vol.9
, pp. 383-389
-
-
Groves, M.R.1
Barford, D.2
-
15
-
-
0033954256
-
The Protein Data Bank
-
H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, and H. Weissig The Protein Data Bank Nucl. Acids Res. 28 2000 235 242
-
(2000)
Nucl. Acids Res.
, vol.28
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
Bhat, T.N.5
Weissig, H.6
-
16
-
-
0034674169
-
A minimum folding unit in the ankyrin repeat protein p16(INK4)
-
B. Zhang, and Z. Peng A minimum folding unit in the ankyrin repeat protein p16(INK4) J. Mol. Biol. 299 2000 1121 1132
-
(2000)
J. Mol. Biol.
, vol.299
, pp. 1121-1132
-
-
Zhang, B.1
Peng, Z.2
-
17
-
-
0033613908
-
Stability and folding of the tumour suppressor protein p16
-
K.S. Tang, B.J. Guralnick, W.K. Wang, A.R. Fersht, and L.S. Itzhaki Stability and folding of the tumour suppressor protein p16 J. Mol. Biol. 285 1999 1869 1886
-
(1999)
J. Mol. Biol.
, vol.285
, pp. 1869-1886
-
-
Tang, K.S.1
Guralnick, B.J.2
Wang, W.K.3
Fersht, A.R.4
Itzhaki, L.S.5
-
18
-
-
0036298327
-
Equilibrium folding and stability of myotrophin: A model ankyrin repeat protein
-
L.K. Mosavi, S. Williams, and Z.Y. Peng Zy Equilibrium folding and stability of myotrophin: a model ankyrin repeat protein J. Mol. Biol. 320 2002 165 170
-
(2002)
J. Mol. Biol.
, vol.320
, pp. 165-170
-
-
Mosavi, L.K.1
Williams, S.2
Peng Zy, Z.Y.3
-
19
-
-
0035807936
-
Studies of the ankyrin repeats of the Drosophila melanogaster Notch receptor. 2. Solution stability and cooperativity of unfolding
-
M.E. Zweifel, and D. Barrick Studies of the ankyrin repeats of the Drosophila melanogaster Notch receptor. 2. Solution stability and cooperativity of unfolding Biochemistry 40 2001 14357 14367
-
(2001)
Biochemistry
, vol.40
, pp. 14357-14367
-
-
Zweifel, M.E.1
Barrick, D.2
-
20
-
-
2942615093
-
The folding and dimerization of HIV-1 protease: Evidence for a stable monomer from simulations
-
Y. Levy, A. Caflisch, J.N. Onuchic, and P.G. Wolynes The folding and dimerization of HIV-1 protease: evidence for a stable monomer from simulations J. Mol. Biol. 340 2004 67 79
-
(2004)
J. Mol. Biol.
, vol.340
, pp. 67-79
-
-
Levy, Y.1
Caflisch, A.2
Onuchic, J.N.3
Wolynes, P.G.4
-
22
-
-
22244447465
-
Overcoming residual frustration in domain-swapping: The roles of disulfide bonds in dimerization and aggregation
-
S.S. Cho, Y. Levy, J.N. Onuchic, and P.G. Wolynes Overcoming residual frustration in domain-swapping: the roles of disulfide bonds in dimerization and aggregation Phys. Biol. 2 2005 S44 S55
-
(2005)
Phys. Biol.
, vol.2
-
-
Cho, S.S.1
Levy, Y.2
Onuchic, J.N.3
Wolynes, P.G.4
-
23
-
-
0000355428
-
Respective roles of short- and long-range interactions in protein folding
-
N. Go, and H. Taketomi Respective roles of short- and long-range interactions in protein folding Proc. Natl Acad. Sci. USA 75 1978 559 563
-
(1978)
Proc. Natl Acad. Sci. USA
, vol.75
, pp. 559-563
-
-
Go, N.1
Taketomi, H.2
-
24
-
-
0002688755
-
Modern methods of analyzing Monte Carlo computer-simulations
-
R.H. Swendsen Modern methods of analyzing Monte Carlo computer-simulations Phys. A 194 1993 53 62
-
(1993)
Phys. a
, vol.194
, pp. 53-62
-
-
Swendsen, R.H.1
-
25
-
-
18744380008
-
Consensus-derived structural determinants of the ankyrin repeat motif
-
L.K. Mosavi, D.L. Minor Jr, and Z.Y. Peng Consensus-derived structural determinants of the ankyrin repeat motif Proc. Natl Acad. Sci. USA 99 2002 16029 16034
-
(2002)
Proc. Natl Acad. Sci. USA
, vol.99
, pp. 16029-16034
-
-
Mosavi, L.K.1
Minor Jr., D.L.2
Peng, Z.Y.3
-
26
-
-
0001563395
-
On the transition coordinate for protein folding
-
R. Du, V.S. Pande, A.Y. Grosberg, T. Tanaka, and E.S. Shakhnovich On the transition coordinate for protein folding J. Chem. Phys. 108 1998 334 350
-
(1998)
J. Chem. Phys.
, vol.108
, pp. 334-350
-
-
Du, R.1
Pande, V.S.2
Grosberg, A.Y.3
Tanaka, T.4
Shakhnovich, E.S.5
-
27
-
-
0027769876
-
A new regulatory motif in cell-cycle control causing specific inhibition of cyclin D/CDK4
-
M. Serrano, G.J. Hannon, and D. Beach A new regulatory motif in cell-cycle control causing specific inhibition of cyclin D/CDK4 Nature 366 1993 704 707
-
(1993)
Nature
, vol.366
, pp. 704-707
-
-
Serrano, M.1
Hannon, G.J.2
Beach, D.3
-
29
-
-
0037228879
-
Sequential unfolding of ankyrin repeats in tumor suppressor p16
-
K.S. Tang, A.R. Fersht, and L.S. Itzhaki Sequential unfolding of ankyrin repeats in tumor suppressor p16 Structure (Camb) 11 2003 67 73
-
(2003)
Structure (Camb)
, vol.11
, pp. 67-73
-
-
Tang, K.S.1
Fersht, A.R.2
Itzhaki, L.S.3
-
30
-
-
0037452697
-
Designed to be stable: Crystal structure of a consensus ankyrin repeat protein
-
A. Kohl, H.K. Binz, P. Forrer, M.T. Stumpp, A. Pluckthun, and M.G. Grutter Designed to be stable: crystal structure of a consensus ankyrin repeat protein Proc. Natl Acad. Sci. USA 100 2003 1700 1705
-
(2003)
Proc. Natl Acad. Sci. USA
, vol.100
, pp. 1700-1705
-
-
Kohl, A.1
Binz, H.K.2
Forrer, P.3
Stumpp, M.T.4
Pluckthun, A.5
Grutter, M.G.6
-
31
-
-
0042780350
-
Designing repeat proteins: Well-expressed, soluble and stable proteins from combinatorial libraries of consensus ankyrin repeat proteins
-
H.K. Binz, M.T. Stumpp, P. Forrer, P. Amstutz, and A. Pluckthun Designing repeat proteins: well-expressed, soluble and stable proteins from combinatorial libraries of consensus ankyrin repeat proteins J. Mol. Biol. 332 2003 489 503
-
(2003)
J. Mol. Biol.
, vol.332
, pp. 489-503
-
-
Binz, H.K.1
Stumpp, M.T.2
Forrer, P.3
Amstutz, P.4
Pluckthun, A.5
-
32
-
-
2342624119
-
High-affinity binders selected from designed ankyrin repeat protein libraries
-
H.K. Binz, P. Amstutz, A. Kohl, M.T. Stumpp, C. Briand, and P. Forrer High-affinity binders selected from designed ankyrin repeat protein libraries Nature Biotechnol. 22 2004 575 582
-
(2004)
Nature Biotechnol.
, vol.22
, pp. 575-582
-
-
Binz, H.K.1
Amstutz, P.2
Kohl, A.3
Stumpp, M.T.4
Briand, C.5
Forrer, P.6
-
33
-
-
0023724778
-
I kappa B: A specific inhibitor of the NF-kappa B transcription factor
-
P.A. Baeuerle, and D. Baltimore I kappa B: a specific inhibitor of the NF-kappa B transcription factor Science 242 1988 540 546
-
(1988)
Science
, vol.242
, pp. 540-546
-
-
Baeuerle, P.A.1
Baltimore, D.2
-
34
-
-
0029874138
-
NF-kappa B and I kappa B proteins: New discoveries and insights
-
A.S. Baldwin Jr NF-kappa B and I kappa B proteins: new discoveries and insights Annu. Rev. Immunol. 14 1996 649 683
-
(1996)
Annu. Rev. Immunol.
, vol.14
, pp. 649-683
-
-
Baldwin, A.S.1
Jr2
-
35
-
-
0032217264
-
Structure of an IkappaBalpha/NF-kappaB complex
-
M.D. Jacobs, and S.C. Harrison Structure of an IkappaBalpha/NF-kappaB complex Cell 95 1998 749 758
-
(1998)
Cell
, vol.95
, pp. 749-758
-
-
Jacobs, M.D.1
Harrison, S.C.2
-
36
-
-
0032217268
-
The crystal structure of the IkappaBalpha/NF-kappaB complex reveals mechanisms of NF-kappaB inactivation
-
T. Huxford, D.B. Huang, S. Malek, and G. Ghosh The crystal structure of the IkappaBalpha/NF-kappaB complex reveals mechanisms of NF-kappaB inactivation Cell 95 1998 759 770
-
(1998)
Cell
, vol.95
, pp. 759-770
-
-
Huxford, T.1
Huang, D.B.2
Malek, S.3
Ghosh, G.4
-
37
-
-
0036931719
-
Solvent exposed non-contacting amino acids play a critical role in NF-kappaB/IkappaBalpha complex formation
-
T. Huxford, D. Mishler, C.B. Phelps, D.B. Huang, L.L. Sengchanthalangsy, and R. Reeves Solvent exposed non-contacting amino acids play a critical role in NF-kappaB/IkappaBalpha complex formation J. Mol. Biol. 324 2002 587 597
-
(2002)
J. Mol. Biol.
, vol.324
, pp. 587-597
-
-
Huxford, T.1
Mishler, D.2
Phelps, C.B.3
Huang, D.B.4
Sengchanthalangsy, L.L.5
Reeves, R.6
-
38
-
-
3042628330
-
Biophysical characterization of the free IkappaBalpha ankyrin repeat domain in solution
-
C.H. Croy, S. Bergqvist, T. Huxford, G. Ghosh, and E.A. Komives Biophysical characterization of the free IkappaBalpha ankyrin repeat domain in solution Protein Sci. 13 2004 1767 1777
-
(2004)
Protein Sci.
, vol.13
, pp. 1767-1777
-
-
Croy, C.H.1
Bergqvist, S.2
Huxford, T.3
Ghosh, G.4
Komives, E.A.5
-
39
-
-
0036438808
-
Limits of cooperativity in a structurally modular protein: Response of the Notch ankyrin domain to analogous alanine substitutions in each repeat
-
C.M. Bradley, and D. Barrick Limits of cooperativity in a structurally modular protein: response of the Notch ankyrin domain to analogous alanine substitutions in each repeat J. Mol. Biol. 324 2002 373 386
-
(2002)
J. Mol. Biol.
, vol.324
, pp. 373-386
-
-
Bradley, C.M.1
Barrick, D.2
-
40
-
-
4644306518
-
An experimentally determined protein folding energy landscape
-
C.C. Mello, and D. Barrick An experimentally determined protein folding energy landscape Proc. Natl Acad. Sci. USA 101 2004 14102 14107
-
(2004)
Proc. Natl Acad. Sci. USA
, vol.101
, pp. 14102-14107
-
-
Mello, C.C.1
Barrick, D.2
-
41
-
-
0028947257
-
Funnels, pathways, and the energy landscape of protein folding: A synthesis
-
J.D. Bryngelson, J.N. Onuchic, N.D. Socci, and P.G. Wolynes Funnels, pathways, and the energy landscape of protein folding: a synthesis Proteins: Struct. Funct. Genet. 21 1995 167 195
-
(1995)
Proteins: Struct. Funct. Genet.
, vol.21
, pp. 167-195
-
-
Bryngelson, J.D.1
Onuchic, J.N.2
Socci, N.D.3
Wolynes, P.G.4
-
42
-
-
0036023918
-
Understanding protein folding with energy landscape theory. Part I: Basic concepts
-
S.S. Plotkin, and J.N. Onuchic Understanding protein folding with energy landscape theory. Part I: basic concepts Quart. Rev. Biophys. 35 2002 111 167
-
(2002)
Quart. Rev. Biophys.
, vol.35
, pp. 111-167
-
-
Plotkin, S.S.1
Onuchic, J.N.2
-
43
-
-
2442706456
-
The ankyrin repeat as molecular architecture for protein recognition
-
L.K. Mosavi, T.J. Cammett, D.C. Desrosiers, and Z.Y. Peng The ankyrin repeat as molecular architecture for protein recognition Protein Sci. 13 2004 1435 1448
-
(2004)
Protein Sci.
, vol.13
, pp. 1435-1448
-
-
Mosavi, L.K.1
Cammett, T.J.2
Desrosiers, D.C.3
Peng, Z.Y.4
-
44
-
-
0033585104
-
Tumor suppressor INK4: Comparisons of conformational properties between p16(INK4A) and p18(INK4C)
-
C. Yuan, J. Li, T.L. Selby, I.J. Byeon, and M.D. Tsai Tumor suppressor INK4: comparisons of conformational properties between p16(INK4A) and p18(INK4C) J. Mol. Biol. 294 1999 201 211
-
(1999)
J. Mol. Biol.
, vol.294
, pp. 201-211
-
-
Yuan, C.1
Li, J.2
Selby, T.L.3
Byeon, I.J.4
Tsai, M.D.5
-
45
-
-
0142210110
-
Structure and stability of the ankyrin domain of the Drosophila Notch receptor
-
M.E. Zweifel, D.J. Leahy, F.M. Hughson, and D. Barrick Structure and stability of the ankyrin domain of the Drosophila Notch receptor Protein Sci. 12 2003 2622 2632
-
(2003)
Protein Sci.
, vol.12
, pp. 2622-2632
-
-
Zweifel, M.E.1
Leahy, D.J.2
Hughson, F.M.3
Barrick, D.4
-
46
-
-
0000122573
-
PHYLIP - Phylogeny inference package
-
J. Felsenstein PHYLIP - Phylogeny inference package Cladistics 5 1989 164 166
-
(1989)
Cladistics
, vol.5
, pp. 164-166
-
-
Felsenstein, J.1
-
47
-
-
0037452701
-
Associative memory Hamiltonians for structure prediction without homology: Alpha/beta proteins
-
C. Hardin, M.P. Eastwood, M.C. Prentiss, Z. Luthey-Schulten, and P.G. Wolynes Associative memory Hamiltonians for structure prediction without homology: alpha/beta proteins Proc. Natl Acad. Sci. USA 100 2003 1679 1684
-
(2003)
Proc. Natl Acad. Sci. USA
, vol.100
, pp. 1679-1684
-
-
Hardin, C.1
Eastwood, M.P.2
Prentiss, M.C.3
Luthey-Schulten, Z.4
Wolynes, P.G.5
|