-
1
-
-
0035887270
-
Brinker requires two corepressors for maximal and versatile repression in Dpp signaling
-
P. Hasson B. Muller K. Basler Z. Paroush Brinker requires two corepressors for maximal and versatile repression in Dpp signaling EMBO J. 2001 20 20 5725 36
-
(2001)
EMBO J.
, vol.20
, Issue.20
, pp. 5725-36
-
-
Hasson, P.1
Muller, B.2
Basler, K.3
Paroush, Z.4
-
2
-
-
0034669166
-
Direct transcriptional control of the Dpp target omb by the DNA binding protein Brinker
-
R. Sivasankaran M. A. Vigano B. Muller M. Affolter K. Basler Direct transcriptional control of the Dpp target omb by the DNA binding protein Brinker EMBO J. 2000 19 22 6162 72
-
(2000)
EMBO J.
, vol.19
, Issue.22
, pp. 6162-72
-
-
Sivasankaran, R.1
Vigano, M.A.2
Muller, B.3
Affolter, M.4
Basler, K.5
-
3
-
-
33746786029
-
DNA recognition by the brinker repressor - An extreme case of coupling between binding and folding
-
F. Cordier B. Hartmann M. Rogowski M. Affolter S. Grzesiek DNA recognition by the brinker repressor - an extreme case of coupling between binding and folding J. Mol. Biol. 2006 361 4 659 72
-
(2006)
J. Mol. Biol.
, vol.361
, Issue.4
, pp. 659-72
-
-
Cordier, F.1
Hartmann, B.2
Rogowski, M.3
Affolter, M.4
Grzesiek, S.5
-
4
-
-
73949144611
-
Toward a quantitative theory of intrinsically disordered proteins and their function
-
J. Liu J. R. Faeder C. J. Camacho Toward a quantitative theory of intrinsically disordered proteins and their function Proc. Natl. Acad. Sci. U.S.A. 2009 106 47 19819 23
-
(2009)
Proc. Natl. Acad. Sci. U.S.A.
, vol.106
, Issue.47
, pp. 19819-23
-
-
Liu, J.1
Faeder, J.R.2
Camacho, C.J.3
-
5
-
-
0035814889
-
Linked folding and anion binding of the Bacillus subtilis ribonuclease P protein
-
C. H. Henkels J. C. Kurz C. A. Fierke T. G. Oas Linked folding and anion binding of the Bacillus subtilis ribonuclease P protein Biochemistry 2001 40 9 2777 2789
-
(2001)
Biochemistry
, vol.40
, Issue.9
, pp. 2777-2789
-
-
Henkels, C.H.1
Kurz, J.C.2
Fierke, C.A.3
Oas, T.G.4
-
6
-
-
33745428137
-
Ligation-state hydrogen exchange: Coupled binding and folding equilibria in ribonuclease P protein
-
C. H. Henkels T. G. Oas Ligation-state hydrogen exchange: Coupled binding and folding equilibria in ribonuclease P protein J. Am. Chem. Soc. 2006 128 24 7772 7781
-
(2006)
J. Am. Chem. Soc.
, vol.128
, Issue.24
, pp. 7772-7781
-
-
Henkels, C.H.1
Oas, T.G.2
-
7
-
-
34250821717
-
Mechanism of coupled folding and binding of an intrinsically disordered protein
-
K. Sugase H. J. Dyson P. E. Wright Mechanism of coupled folding and binding of an intrinsically disordered protein Nature 2007 447 7147 1021 5
-
(2007)
Nature
, vol.447
, Issue.7147
, pp. 1021-5
-
-
Sugase, K.1
Dyson, H.J.2
Wright, P.E.3
-
8
-
-
42949161558
-
Binding-induced folding of a natively unstructured transcription factor
-
A. G. Turjanski J. S. Gutkind R. B. Best G. Hummer Binding-induced folding of a natively unstructured transcription factor PLoS Comput. Biol. 2008 4 4 e1000060
-
(2008)
PLoS Comput. Biol.
, vol.4
, Issue.4
, pp. 1000060
-
-
Turjanski, A.G.1
Gutkind, J.S.2
Best, R.B.3
Hummer, G.4
-
10
-
-
0028922586
-
LIGPLOT: A program to generate schematic diagrams of protein-ligand interactions
-
A. C. Wallace R. A. Laskowski J. M. Thornton LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions Protein Eng., Des. Sel. 1995 8 2 127 34
-
(1995)
Protein Eng., Des. Sel.
, vol.8
, Issue.2
, pp. 127-34
-
-
Wallace, A.C.1
Laskowski, R.A.2
Thornton, J.M.3
-
11
-
-
0026511656
-
The folding of an enzyme. I. Theory of protein engineering analysis of stability and pathway of protein folding
-
A. R. Fersht A. Matouschek L. Serrano The folding of an enzyme. I. Theory of protein engineering analysis of stability and pathway of protein folding J. Mol. Biol. 1992 224 3 771 82
-
(1992)
J. Mol. Biol.
, vol.224
, Issue.3
, pp. 771-82
-
-
Fersht, A.R.1
Matouschek, A.2
Serrano, L.3
-
12
-
-
34547651105
-
Searching for multiple folding pathways of a nearly symmetrical protein: Temperature dependent phi-value analysis of the B domain of protein A
-
S. Sato A. R. Fersht Searching for multiple folding pathways of a nearly symmetrical protein: temperature dependent phi-value analysis of the B domain of protein A J. Mol. Biol. 2007 372 1 254 67
-
(2007)
J. Mol. Biol.
, vol.372
, Issue.1
, pp. 254-67
-
-
Sato, S.1
Fersht, A.R.2
-
13
-
-
0034652206
-
Transition-state structure as a unifying basis in protein-folding mechanisms: Contact order, chain topology, stability, and the extended nucleus mechanism
-
A. R. Fersht Transition-state structure as a unifying basis in protein-folding mechanisms: contact order, chain topology, stability, and the extended nucleus mechanism Proc. Natl. Acad. Sci. U. S. A. 2000 97 4 1525 9
-
(2000)
Proc. Natl. Acad. Sci. U. S. A.
, vol.97
, Issue.4
, pp. 1525-9
-
-
Fersht, A.R.1
-
15
-
-
0034872511
-
Transition states and the meaning of phi-values in protein folding kinetics
-
S. B. Ozkan I. Bahar K. A. Dill Transition states and the meaning of phi-values in protein folding kinetics Nat. Struct. Biol. 2001 8 765 769
-
(2001)
Nat. Struct. Biol.
, vol.8
, pp. 765-769
-
-
Ozkan, S.B.1
Bahar, I.2
Dill, K.A.3
-
16
-
-
0029981188
-
Structure of the transition state for folding of a protein derived from experiment and simulation
-
V. Daggett A. J. Li L. S. Itzhaki D. E. Otzen A. R. Fersht Structure of the transition state for folding of a protein derived from experiment and simulation J. Mol. Biol. 1996 257 2 430 440
-
(1996)
J. Mol. Biol.
, vol.257
, Issue.2
, pp. 430-440
-
-
Daggett, V.1
Li, A.J.2
Itzhaki, L.S.3
Otzen, D.E.4
Fersht, A.R.5
-
17
-
-
0031465967
-
"New view" of protein folding reconciled with the old through multiple unfolding simulations
-
T. Lazaridis M. Karplus "New view" of protein folding reconciled with the old through multiple unfolding simulations Science 1997 278 5345 1928 31
-
(1997)
Science
, vol.278
, Issue.5345
, pp. 1928-31
-
-
Lazaridis, T.1
Karplus, M.2
-
18
-
-
1642384392
-
Folding for binding or binding for folding?
-
A. Caflisch Folding for binding or binding for folding? Trends Biotechnol. 2003 21 10 423 5
-
(2003)
Trends Biotechnol.
, vol.21
, Issue.10
, pp. 423-5
-
-
Caflisch, A.1
-
20
-
-
33846381622
-
Direct observation of microscopic reversibility in single-molecule protein folding
-
R. Day V. Daggett Direct observation of microscopic reversibility in single-molecule protein folding J. Mol. Biol. 2007 366 2 677 86
-
(2007)
J. Mol. Biol.
, vol.366
, Issue.2
, pp. 677-86
-
-
Day, R.1
Daggett, V.2
-
21
-
-
46849113841
-
Microscopic reversibility of protein folding in molecular dynamics simulations of the engrailed homeodomain
-
M. E. McCully D. A. Beck V. Daggett Microscopic reversibility of protein folding in molecular dynamics simulations of the engrailed homeodomain Biochemistry 2008 47 27 7079 89
-
(2008)
Biochemistry
, vol.47
, Issue.27
, pp. 7079-89
-
-
McCully, M.E.1
Beck, D.A.2
Daggett, V.3
-
22
-
-
45849095234
-
Biochemistry. How do proteins interact?
-
D. D. Boehr P. E. Wright Biochemistry. How do proteins interact? Science 2008 320 5882 1429 30
-
(2008)
Science
, vol.320
, Issue.5882
, pp. 1429-30
-
-
Boehr, D.D.1
Wright, P.E.2
-
23
-
-
0001858251
-
Application of a Theory of Enzyme Specificity to Protein Synthesis
-
D. E. Koshland Application of a Theory of Enzyme Specificity to Protein Synthesis Proc. Natl. Acad. Sci. U. S. A. 1958 44 2 98 104
-
(1958)
Proc. Natl. Acad. Sci. U. S. A.
, vol.44
, Issue.2
, pp. 98-104
-
-
Koshland, D.E.1
-
25
-
-
0036147568
-
Multiple diverse ligands binding at a single protein site: A matter of pre-existing populations
-
B. Ma M. Shatsky H. J. Wolfson R. Nussinov Multiple diverse ligands binding at a single protein site: a matter of pre-existing populations Protein Sci. 2009 11 2 184 97
-
(2009)
Protein Sci.
, vol.11
, Issue.2
, pp. 184-97
-
-
Ma, B.1
Shatsky, M.2
Wolfson, H.J.3
Nussinov, R.4
-
26
-
-
0033970020
-
Folding and binding cascades: Dynamic landscapes and population shifts
-
S. Kumar B. Ma C. J. Tsai N. Sinha R. Nussinov Folding and binding cascades: dynamic landscapes and population shifts Protein Sci. 2000 9 1 10 9
-
(2000)
Protein Sci.
, vol.9
, Issue.1
, pp. 10-9
-
-
Kumar, S.1
Ma, B.2
Tsai, C.J.3
Sinha, N.4
Nussinov, R.5
-
27
-
-
75149141847
-
Mechanisms of transcription factor selectivity
-
Y. Pan C. J. Tsai B. Ma R. Nussinov Mechanisms of transcription factor selectivity Trends Genet. 2010 26 2 75 83
-
(2010)
Trends Genet.
, vol.26
, Issue.2
, pp. 75-83
-
-
Pan, Y.1
Tsai, C.J.2
Ma, B.3
Nussinov, R.4
-
28
-
-
70350782360
-
How do transcription factors select specific binding sites in the genome?
-
Y. Pan C. J. Tsai B. Ma R. Nussinov How do transcription factors select specific binding sites in the genome? Nat. Struct. Mol. Biol. 2009 16 11 1118 20
-
(2009)
Nat. Struct. Mol. Biol.
, vol.16
, Issue.11
, pp. 1118-20
-
-
Pan, Y.1
Tsai, C.J.2
Ma, B.3
Nussinov, R.4
-
29
-
-
73349117207
-
Conformational selection and induced fit mechanism underlie specificity in noncovalent interactions with ubiquitin
-
T. Wlodarski B. Zagrovic Conformational selection and induced fit mechanism underlie specificity in noncovalent interactions with ubiquitin Proc. Natl. Acad. Sci. U. S. A. 2009 106 19351 19364
-
(2009)
Proc. Natl. Acad. Sci. U. S. A.
, vol.106
, pp. 19351-19364
-
-
Wlodarski, T.1
Zagrovic, B.2
-
30
-
-
9244260409
-
-
University of California, San Francisco
-
D. A. Case, T. A. Darden, T. E. Cheatham, C. L. Simmerling, III, J. Wang, R. E. Duke, R. Luo, K. M. Merz, B. Wang, D. A. Pearlman, M. Crowley, S. Brozell, V. Tsui, H. Gohlke, J. Mongan, V. Hornak, G. Cui, P. Beroza, C. Schafmeister, J. W. Caldwell, W. S. Ross and P. A. Kollman, AMBER 8, University of California, San Francisco, 2004
-
(2004)
AMBER 8
-
-
Case, D.A.1
Darden, T.A.2
Cheatham, T.E.3
Simmerling III, C.L.4
Wang, J.5
Duke, R.E.6
Luo, R.7
Merz, K.M.8
Wang, B.9
Pearlman, D.A.10
Crowley, M.11
Brozell, S.12
Tsui, V.13
Gohlke, H.14
Mongan, J.15
Hornak, V.16
Cui, G.17
Beroza, P.18
Schafmeister, C.19
Caldwell, J.W.20
Ross, W.S.21
Kollman, P.A.22
more..
-
32
-
-
33846823909
-
Particle mesh Ewald: An N log(N) method for Ewald sums in large systems
-
T. Darden D. York L. Pedersen 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
-
33
-
-
0242663237
-
A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations
-
Y. Duan C. Wu S. Chowdhury M. C. Lee G. Xiong W. Zhang R. Yang P. Cieplak R. Luo T. Lee J. Caldwell J. Wang P. Kollman A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations J. Comput. Chem. 2003 24 16 1999 2012
-
(2003)
J. Comput. Chem.
, vol.24
, Issue.16
, pp. 1999-2012
-
-
Duan, Y.1
Wu, C.2
Chowdhury, S.3
Lee, M.C.4
Xiong, G.5
Zhang, W.6
Yang, R.7
Cieplak, P.8
Luo, R.9
Lee, T.10
Caldwell, J.11
Wang, J.12
Kollman, P.13
-
34
-
-
33646940952
-
Numerical integration of Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
-
J. P. Rychaert G. Ciccotti H. J. C. Berendsen Numerical integration of Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes J. Comput. Phys. 1977 23 327 341
-
(1977)
J. Comput. Phys.
, vol.23
, pp. 327-341
-
-
Rychaert, J.P.1
Ciccotti, G.2
Berendsen, H.J.C.3
-
36
-
-
0033529908
-
Molecular dynamics simulations of unfolding and refolding of a beta-hairpin fragment of protein G
-
V. S. Pande D. S. Rokhsar Molecular dynamics simulations of unfolding and refolding of a beta-hairpin fragment of protein G Proc. Natl. Acad. Sci. U. S. A. 1999 96 16 9062 7
-
(1999)
Proc. Natl. Acad. Sci. U. S. A.
, vol.96
, Issue.16
, pp. 9062-7
-
-
Pande, V.S.1
Rokhsar, D.S.2
-
37
-
-
0037076334
-
Molecular dynamics simulations of protein folding from the transition state
-
J. Gsponer A. Caflisch Molecular dynamics simulations of protein folding from the transition state Proc. Natl. Acad. Sci. U. S. A. 2002 99 10 6719 24
-
(2002)
Proc. Natl. Acad. Sci. U. S. A.
, vol.99
, Issue.10
, pp. 6719-24
-
-
Gsponer, J.1
Caflisch, A.2
-
38
-
-
10044265557
-
Dimerization of the p53 oligomerization domain: Identification of a folding nucleus by molecular dynamics simulations
-
L. T. Chong C. D. Snow Y. M. Rhee V. S. Pande Dimerization of the p53 oligomerization domain: identification of a folding nucleus by molecular dynamics simulations J. Mol. Biol. 2005 345 4 869 78
-
(2005)
J. Mol. Biol.
, vol.345
, Issue.4
, pp. 869-78
-
-
Chong, L.T.1
Snow, C.D.2
Rhee, Y.M.3
Pande, V.S.4
-
39
-
-
57749174350
-
Mechanism of coupled folding and binding in the siRNA-PAZ complex
-
H. F. Chen Mechanism of coupled folding and binding in the siRNA-PAZ complex J. Chem. Theory Comput. 2008 4 1360 1368
-
(2008)
J. Chem. Theory Comput.
, vol.4
, pp. 1360-1368
-
-
Chen, H.F.1
-
40
-
-
68349133281
-
Molecular dynamics simulation of phosphorylated KID post-translational modification
-
H. F. Chen Molecular dynamics simulation of phosphorylated KID post-translational modification PLoS One 2009 4 8 e6516
-
(2009)
PLoS One
, vol.4
, Issue.8
, pp. 6516
-
-
Chen, H.F.1
-
41
-
-
33947252405
-
Binding induced folding in p53-MDM2 complex
-
H. F. Chen R. Luo Binding induced folding in p53-MDM2 complex J. Am. Chem. Soc. 2007 129 10 2930 7
-
(2007)
J. Am. Chem. Soc.
, vol.129
, Issue.10
, pp. 2930-7
-
-
Chen, H.F.1
Luo, R.2
-
43
-
-
77951170511
-
Induced fit or conformational selection for RNA/U1A folding
-
F. Qin Y. Chen M. Wu Y. Li J. Zhang H. F. Chen Induced fit or conformational selection for RNA/U1A folding RNA 2010 16 1053 1061
-
(2010)
RNA
, vol.16
, pp. 1053-1061
-
-
Qin, F.1
Chen, Y.2
Wu, M.3
Li, Y.4
Zhang, J.5
Chen, H.F.6
-
44
-
-
57749195950
-
Aggregation mechanism investigation of the GIFQINS cross-beta amyloid fibril
-
H. F. Chen Aggregation mechanism investigation of the GIFQINS cross-beta amyloid fibril Comput. Biol. Chem. 2009 33 1 41 5
-
(2009)
Comput. Biol. Chem.
, vol.33
, Issue.1
, pp. 41-5
-
-
Chen, H.F.1
-
45
-
-
0028264860
-
Molecular-dynamics simulation of protein denaturation-solvation of the hydrophobic cores and secondary structure of barnase
-
A. Caflisch M. Karplus Molecular-dynamics simulation of protein denaturation-solvation of the hydrophobic cores and secondary structure of barnase Proc. Natl. Acad. Sci. U. S. A. 1994 91 5 1746 1750
-
(1994)
Proc. Natl. Acad. Sci. U. S. A.
, vol.91
, Issue.5
, pp. 1746-1750
-
-
Caflisch, A.1
Karplus, M.2
-
46
-
-
0035252350
-
Three key residues form a critical contact network in a protein folding transition state
-
M. Vendruscolo E. Paci C. M. Dobson M. Karplus Three key residues form a critical contact network in a protein folding transition state Nature 2001 409 6820 641 645
-
(2001)
Nature
, vol.409
, Issue.6820
, pp. 641-645
-
-
Vendruscolo, M.1
Paci, E.2
Dobson, C.M.3
Karplus, M.4
|