-
1
-
-
18644368600
-
The free energy landscape of A-DNA to B-DNA conversion in aqueous solution
-
N.K. Banavali, and B. Roux The free energy landscape of A-DNA to B-DNA conversion in aqueous solution J. Am. Chem. Soc. 127 2005 6866 6876
-
(2005)
J. Am. Chem. Soc.
, vol.127
, pp. 6866-6876
-
-
Banavali, N.K.1
Roux, B.2
-
2
-
-
0001655657
-
Finite representation of an infinite bulk system: Solvent boundary potential for computer simulations
-
D. Beglov, and B. Roux Finite representation of an infinite bulk system: solvent boundary potential for computer simulations J. Chem. Phys. 100 1994 9050 9063
-
(1994)
J. Chem. Phys.
, vol.100
, pp. 9050-9063
-
-
Beglov, D.1
Roux, B.2
-
3
-
-
84986512474
-
CHARMM: A program for macromolecular energy minimization and dynamics calculations
-
B. Brooks, R. Bruccoleri, B. Olafson, D. States, S. Swaminathan, and M. Karplus CHARMM: A program for macromolecular energy minimization and dynamics calculations J. Comput. Chem. 4 1983 187 217
-
(1983)
J. Comput. Chem.
, vol.4
, pp. 187-217
-
-
Brooks, B.1
Bruccoleri, R.2
Olafson, B.3
States, D.4
Swaminathan, S.5
Karplus, M.6
-
4
-
-
0029896163
-
Regulation, substrates and functions of Src
-
M. Brown, and J. Cooper Regulation, substrates and functions of Src Biochim. Biophys. Acta 1287 1996 121 149
-
(1996)
Biochim. Biophys. Acta
, vol.1287
, pp. 121-149
-
-
Brown, M.1
Cooper, J.2
-
5
-
-
0034327349
-
Prediction of tight turns and their types in proteins
-
K.-C. Chou Prediction of tight turns and their types in proteins Anal. Biochem. 286 2000 1 16
-
(2000)
Anal. Biochem.
, vol.286
, pp. 1-16
-
-
Chou, K.-C.1
-
6
-
-
20444399897
-
The crystal structure of a c-src complex in an active conformation suggests possible steps in c-Src activation
-
S.W. Cowan-Jacob, G. Fendrich, P.W. Manley, W. Jahnke, D. Fabbro, J. Liebetanz, and T. Meyer The crystal structure of a c-src complex in an active conformation suggests possible steps in c-Src activation Structure 13 2005 861 871
-
(2005)
Structure
, vol.13
, pp. 861-871
-
-
Cowan-Jacob, S.W.1
Fendrich, G.2
Manley, P.W.3
Jahnke, W.4
Fabbro, D.5
Liebetanz, J.6
Meyer, T.7
-
7
-
-
33846823909
-
Particle Mesh Ewald - An N.log(N) method for Ewald sums in large systems
-
T. Darden, D. York, and L. Pedersen Particle Mesh Ewald - an N.log(N) method for Ewald sums in large systems J. Chem. Phys. 98 1993 10089 10092
-
(1993)
J. Chem. Phys.
, vol.98
, pp. 10089-10092
-
-
Darden, T.1
York, D.2
Pedersen, L.3
-
8
-
-
0003639599
-
-
PhD thesis, Harvard University, Cambridge, Massachusetts.
-
Field, M.J., and Karplus, M. (1992). CRYSTAL: a program for crystal calculations in CHARMM. PhD thesis, Harvard University, Cambridge, Massachusetts.
-
(1992)
CRYSTAL: A Program for Crystal Calculations in CHARMM
-
-
Field, M.J.1
Karplus, M.2
-
9
-
-
0031464009
-
The role of the linker between the SH2 domain and catalytic domain in the regulation and function of Src
-
S. Gonfloni, J. Williams, K. Hattula, A. Weijland, R. Wierenga, and G. Superti-Furga The role of the linker between the SH2 domain and catalytic domain in the regulation and function of Src EMBO J. 16 1997 7261 7271
-
(1997)
EMBO J.
, vol.16
, pp. 7261-7271
-
-
Gonfloni, S.1
Williams, J.2
Hattula, K.3
Weijland, A.4
Wierenga, R.5
Superti-Furga, G.6
-
11
-
-
0027968068
-
CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
-
D. Higgins, J. Thompson, T. Gibson, J.D. Thompson, D.G. Higgins, and T.J. Gibson CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice Nucleic Acids Res. 22 1994 4673 4680
-
(1994)
Nucleic Acids Res.
, vol.22
, pp. 4673-4680
-
-
Higgins, D.1
Thompson, J.2
Gibson, T.3
Thompson, J.D.4
Higgins, D.G.5
Gibson, T.J.6
-
12
-
-
0030766163
-
Crystal structure of the activated insulin receptor tyrosine kinase in complex with peptide substrate and atp analog
-
S. Hubbard Crystal structure of the activated insulin receptor tyrosine kinase in complex with peptide substrate and atp analog EMBO J. 16 1997 5573 5581
-
(1997)
EMBO J.
, vol.16
, pp. 5573-5581
-
-
Hubbard, S.1
-
13
-
-
0028582185
-
Crystal structure of the tyrosine kinase domain of the human insulin receptor
-
S.R. Hubbard, L. Wei, L. Ellis, and W.A. Hendrickson Crystal structure of the tyrosine kinase domain of the human insulin receptor Nature 372 1994 746 754
-
(1994)
Nature
, vol.372
, pp. 746-754
-
-
Hubbard, S.R.1
Wei, L.2
Ellis, L.3
Hendrickson, W.A.4
-
14
-
-
0037013143
-
The conformational plasticity of protein kinases
-
M. Huse, and J. Kuriyan The conformational plasticity of protein kinases Cell 109 2002 275 282
-
(2002)
Cell
, vol.109
, pp. 275-282
-
-
Huse, M.1
Kuriyan, J.2
-
16
-
-
0013863816
-
Comparison of experimental binding data and theoretical models in proteins containing subunits
-
D.E. Koshland Jr., G. Nemethy, and D. Filmer Comparison of experimental binding data and theoretical models in proteins containing subunits Biochemistry 5 1966 365 385
-
(1966)
Biochemistry
, vol.5
, pp. 365-385
-
-
Koshland Jr., D.E.1
Nemethy, G.2
Filmer, D.3
-
17
-
-
84986519238
-
The weighted histogram analysis method for free-energy calculations on biomolecules.1. the method
-
S. Kumar, D. Bouzida, R.H. Swendsen, P.A. Kollman, and J.M. Rosenberg The weighted histogram analysis method for free-energy calculations on biomolecules.1. The method J. Comput. Chem. 13 1992 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
-
18
-
-
0033610850
-
Intramolecular regulatory interactions in the Src family kinase Hck probed by mutagenesis of a conserved tryptophan residue
-
M. Lafevre-Bernt, F. Sicheri, A. Pico, M. Porter, J. Kuriyan, and W.T. Miller Intramolecular regulatory interactions in the Src family kinase Hck probed by mutagenesis of a conserved tryptophan residue J. Biol. Chem. 273 1998 32129 32134
-
(1998)
J. Biol. Chem.
, vol.273
, pp. 32129-32134
-
-
Lafevre-Bernt, M.1
Sicheri, F.2
Pico, A.3
Porter, M.4
Kuriyan, J.5
Miller, W.T.6
-
19
-
-
0033536602
-
Evolutionarily conserved pathways of energetic connectivity in protein families
-
S. Lockless, and R. Ranganathan Evolutionarily conserved pathways of energetic connectivity in protein families Science 286 1999 295 299
-
(1999)
Science
, vol.286
, pp. 295-299
-
-
Lockless, S.1
Ranganathan, R.2
-
20
-
-
0024348319
-
Structural differences between repressed and derepressed forms of p60 c-Src
-
A. MacAuley, and J.A. Cooper Structural differences between repressed and derepressed forms of p60 c-Src Mol. Cell. Biol. 9 1989 2648 2656
-
(1989)
Mol. Cell. Biol.
, vol.9
, pp. 2648-2656
-
-
MacAuley, A.1
Cooper, J.A.2
-
21
-
-
0041784950
-
All-atom empirical potential for molecular modeling and dynamics studies of proteins
-
A. MacKerell Jr., D. Bashford, M. Bellot, R. Dunbrack, J. Evanseck, M. Field, S. Fischer, J. Gao, H. Guo, and S. Ha All-atom empirical potential for molecular modeling and dynamics studies of proteins J. Phys. Chem. B 102 1998 3586 3616
-
(1998)
J. Phys. Chem. B
, vol.102
, pp. 3586-3616
-
-
MacKerell Jr., A.1
Bashford, D.2
Bellot, M.3
Dunbrack, R.4
Evanseck, J.5
Field, M.6
Fischer, S.7
Gao, J.8
Guo, H.9
Ha, S.10
-
22
-
-
0033873929
-
Comparative protein structure modeling of genes and genomes
-
M.A. Marti-Renom, A. Stuart, A. Fiser, R. Sanchez, F. Melo, and A. Sali Comparative protein structure modeling of genes and genomes Annu. Rev. Biophys. Biomol. Struct. 29 2000 291 325
-
(2000)
Annu. Rev. Biophys. Biomol. Struct.
, vol.29
, pp. 291-325
-
-
Marti-Renom, M.A.1
Stuart, A.2
Fiser, A.3
Sanchez, R.4
Melo, F.5
Sali, A.6
-
23
-
-
0242268469
-
Non-linear elasticity, proteinquakes, and the energy landscapes of functional transitions in proteins
-
O. Miyashita, J.N. Onuchic, and P.G. Wolynes Non-linear elasticity, proteinquakes, and the energy landscapes of functional transitions in proteins Proc. Natl. Acad. Sci. USA 100 2003 12570 12575
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 12570-12575
-
-
Miyashita, O.1
Onuchic, J.N.2
Wolynes, P.G.3
-
24
-
-
0031017838
-
Activation of the Src-family tyrosine kinase Hck by SH3 domain displacement
-
I. Moarefi, M. LaFevre-Bernt, F. Sicheri, M. Huse, C. Lee, J. Kuriyan, and W. Miller Activation of the Src-family tyrosine kinase Hck by SH3 domain displacement Nature 385 1997 650 653
-
(1997)
Nature
, vol.385
, pp. 650-653
-
-
Moarefi, I.1
Lafevre-Bernt, M.2
Sicheri, F.3
Huse, M.4
Lee, C.5
Kuriyan, J.6
Miller, W.7
-
25
-
-
78651189765
-
On the nature of allosteric transitions: A plausible model
-
J. Monod, J. Wyman, and J.P. Changeux On the nature of allosteric transitions: a plausible model J. Mol. Biol. 12 1965 88 118
-
(1965)
J. Mol. Biol.
, vol.12
, pp. 88-118
-
-
Monod, J.1
Wyman, J.2
Changeux, J.P.3
-
26
-
-
0034723419
-
Reciprocal regulation of Hck activity by phosphorylation of Tyr(527) and Tyr(416). Effect of introducing a high affnity intramolecular SH2 ligand
-
M. Porter, T. Schindler, J. Kuriyan, and W. Miller Reciprocal regulation of Hck activity by phosphorylation of Tyr(527) and Tyr(416). Effect of introducing a high affnity intramolecular SH2 ligand J. Biol. Chem. 275 2000 2721 2726
-
(2000)
J. Biol. Chem.
, vol.275
, pp. 2721-2726
-
-
Porter, M.1
Schindler, T.2
Kuriyan, J.3
Miller, W.4
-
27
-
-
33646940952
-
Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
-
J.P. Ryckaert, G. Ciccotti, and H.J.C. Berendsen Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes J. Comp. Phys. 23 1977 327 341
-
(1977)
J. Comp. Phys.
, vol.23
, pp. 327-341
-
-
Ryckaert, J.P.1
Ciccotti, G.2
Berendsen, H.J.C.3
-
28
-
-
0033063429
-
Crystal structure of Hck in complex with a Src family-selective tyrosine kinase inhibitor
-
T. Schindler, F. Sicheri, A. Pico, A. Gazit, A. Levitzki, and J. Kuriyan Crystal structure of Hck in complex with a Src family-selective tyrosine kinase inhibitor Mol. Cell 3 1999 639 648
-
(1999)
Mol. Cell
, vol.3
, pp. 639-648
-
-
Schindler, T.1
Sicheri, F.2
Pico, A.3
Gazit, A.4
Levitzki, A.5
Kuriyan, J.6
-
30
-
-
0031034930
-
Crystal structure of the Src family tyrosine kinase Hck
-
F. Sicheri, I. Moarefi, and J. Kuriyan Crystal structure of the Src family tyrosine kinase Hck Nature 385 1997 602 609
-
(1997)
Nature
, vol.385
, pp. 602-609
-
-
Sicheri, F.1
Moarefi, I.2
Kuriyan, J.3
-
31
-
-
0035277126
-
Extension to the weighted histogram analysis method: Combining umbrella sampling with free energy calculations
-
M. Souaille, and B. Roux Extension to the weighted histogram analysis method: combining umbrella sampling with free energy calculations Comput. Phys. Comm. 135 2001 40 57
-
(2001)
Comput. Phys. Comm.
, vol.135
, pp. 40-57
-
-
Souaille, M.1
Roux, B.2
-
32
-
-
0037219686
-
Evolutionarily conserved networks of residues mediate allosteric communication in proteins
-
G.M. Suel, S.W. Lockless, M.A. Wall, and R. Ranganathan Evolutionarily conserved networks of residues mediate allosteric communication in proteins Nat. Struct. Biol. 10 2003 59 69
-
(2003)
Nat. Struct. Biol.
, vol.10
, pp. 59-69
-
-
Suel, G.M.1
Lockless, S.W.2
Wall, M.A.3
Ranganathan, R.4
-
33
-
-
0028773477
-
3 protein kinase structures define a common motif
-
S.S. Taylor, and E. Radzio-Andzelm 3 protein kinase structures define a common motif Structure 2 1994 345 355
-
(1994)
Structure
, vol.2
, pp. 345-355
-
-
Taylor, S.S.1
Radzio-Andzelm, E.2
-
34
-
-
0035937443
-
Two-state allosteric behavior in a single-domain signaling protein
-
B.F. Volkman, D. Lipson, D.E. Wemmer, and D. Kern Two-state allosteric behavior in a single-domain signaling protein Science 291 2001 2429 2433
-
(2001)
Science
, vol.291
, pp. 2429-2433
-
-
Volkman, B.F.1
Lipson, D.2
Wemmer, D.E.3
Kern, D.4
-
35
-
-
0015528157
-
Ligand binding and internal equilibria in proteins
-
G. Weber Ligand binding and internal equilibria in proteins Biochemistry 11 1972 864 878
-
(1972)
Biochemistry
, vol.11
, pp. 864-878
-
-
Weber, G.1
-
36
-
-
0031025991
-
Three-dimensional crystal structure of the tyrosine kinase c-Src
-
W. Xu, S.C. Harrison, and M.J. Eck Three-dimensional crystal structure of the tyrosine kinase c-Src Nature 385 1997 595 602
-
(1997)
Nature
, vol.385
, pp. 595-602
-
-
Xu, W.1
Harrison, S.C.2
Eck, M.J.3
-
37
-
-
0033001789
-
Crystal structures of c-Src reveal features of its autoinhibitory mechanism
-
W. Xu, A. Doshi, M. Lei, M.J. Eck, and M.J. Harrison Crystal structures of c-Src reveal features of its autoinhibitory mechanism Mol. Cell 3 1999 629 638
-
(1999)
Mol. Cell
, vol.3
, pp. 629-638
-
-
Xu, W.1
Doshi, A.2
Lei, M.3
Eck, M.J.4
Harrison, M.J.5
-
38
-
-
16144364951
-
Structural basis for activation of human lymphocyte kinase Lck upon tyrosine phosphorylation
-
H. Yamaguchi, and W. Hendrickson Structural basis for activation of human lymphocyte kinase Lck upon tyrosine phosphorylation Nature 384 1996 484 489
-
(1996)
Nature
, vol.384
, pp. 484-489
-
-
Yamaguchi, H.1
Hendrickson, W.2
-
39
-
-
0035815288
-
Dynamic coupling between the SH2 and SH3 domains of c-Src and Hck underlies their inactivation by C-terminal tyrosine phosphorylation
-
M. Young, S. Gonfloni, G. Superti-Furga, B. Roux, and J. Kuriyan Dynamic coupling between the SH2 and SH3 domains of c-Src and Hck underlies their inactivation by C-terminal tyrosine phosphorylation Cell 105 2001 115 126
-
(2001)
Cell
, vol.105
, pp. 115-126
-
-
Young, M.1
Gonfloni, S.2
Superti-Furga, G.3
Roux, B.4
Kuriyan, J.5
|