-
1
-
-
0035393302
-
Amino acid-base interactions: A three-dimensional analysis of protein-DNA interactions at an atomic level
-
N.M. Luscombe, R.A. Laskowski, and J.M. Thornton Amino acid-base interactions: a three-dimensional analysis of protein-DNA interactions at an atomic level Nucl. Acids Res. 29 2001 2860 2874
-
(2001)
Nucl. Acids Res.
, vol.29
, pp. 2860-2874
-
-
Luscombe, N.M.1
Laskowski, R.A.2
Thornton, J.M.3
-
2
-
-
0028839860
-
Comprehensive analysis of hydrogen bonds in regulatory protein DNA-complexes: In search of common principles
-
Y. Mandel-Gutfreund, O. Schueler, and H. Margalit Comprehensive analysis of hydrogen bonds in regulatory protein DNA-complexes: in search of common principles J. Mol. Biol. 253 1995 370 382
-
(1995)
J. Mol. Biol.
, vol.253
, pp. 370-382
-
-
Mandel-Gutfreund, Y.1
Schueler, O.2
Margalit, H.3
-
3
-
-
0028773281
-
A framework for the DNA-protein recognition code of the probe helix in transcription factors: The chemical and stereochemical rules
-
M. Suzuki A framework for the DNA-protein recognition code of the probe helix in transcription factors: the chemical and stereochemical rules Structure 2 1994 317 326
-
(1994)
Structure
, vol.2
, pp. 317-326
-
-
Suzuki, M.1
-
4
-
-
0033120215
-
Structure-based prediction of DNA target sites by regulatory proteins
-
H. Kono, and A. Sarai Structure-based prediction of DNA target sites by regulatory proteins Proteins: Struct. Funct. Genet. 35 1999 114 131
-
(1999)
Proteins: Struct. Funct. Genet.
, vol.35
, pp. 114-131
-
-
Kono, H.1
Sarai, A.2
-
5
-
-
0034682882
-
Geometric analysis and comparison of protein-DNA interfaces: Why is there no simple code for recognition?
-
C.O. Pabo, and L. Nekludova Geometric analysis and comparison of protein-DNA interfaces: why is there no simple code for recognition? J. Mol. Biol. 301 2000 597 624
-
(2000)
J. Mol. Biol.
, vol.301
, pp. 597-624
-
-
Pabo, C.O.1
Nekludova, L.2
-
7
-
-
0024294636
-
Protein-DNA interaction. No code for recognition
-
B.W. Matthews Protein-DNA interaction. No code for recognition Nature 335 1988 294 295
-
(1988)
Nature
, vol.335
, pp. 294-295
-
-
Matthews, B.W.1
-
8
-
-
0028046895
-
Selection of DNA binding sites for zinc fingers using rationally randomized DNA reveals coded interactions
-
Y. Choo, and A. Klug Selection of DNA binding sites for zinc fingers using rationally randomized DNA reveals coded interactions Proc. Natl Acad. Sci. USA 91 1994 11168 11172
-
(1994)
Proc. Natl Acad. Sci. USA
, vol.91
, pp. 11168-11172
-
-
Choo, Y.1
Klug, A.2
-
9
-
-
0027994717
-
Toward a code for the interactions of zinc fingers with DNA: Selection of randomized fingers displayed on phage
-
Y. Choo, and A. Klug Toward a code for the interactions of zinc fingers with DNA: selection of randomized fingers displayed on phage Proc. Natl Acad. Sci. USA 91 1994 11163 11167
-
(1994)
Proc. Natl Acad. Sci. USA
, vol.91
, pp. 11163-11167
-
-
Choo, Y.1
Klug, A.2
-
10
-
-
0031042082
-
Physical basis of a protein-DNA recognition code
-
Y. Choo, and A. Klug Physical basis of a protein-DNA recognition code Curr. Opin. Struct. Biol. 7 1997 117 125
-
(1997)
Curr. Opin. Struct. Biol.
, vol.7
, pp. 117-125
-
-
Choo, Y.1
Klug, A.2
-
11
-
-
0033524954
-
Analysis of zinc fingers optimized via phage display: Evaluating the utility of a recognition code
-
S.A. Wolfe, H.A. Greisman, E.I. Ramm, and C.O. Pabo Analysis of zinc fingers optimized via phage display: evaluating the utility of a recognition code J. Mol. Biol. 285 1999 1917 1934
-
(1999)
J. Mol. Biol.
, vol.285
, pp. 1917-1934
-
-
Wolfe, S.A.1
Greisman, H.A.2
Ramm, E.I.3
Pabo, C.O.4
-
12
-
-
0035914475
-
Rearrangement of side-chains in a Zif268 mutant highlights the complexities of zinc finger-DNA recognition
-
J.C. Miller, and C.O. Pabo Rearrangement of side-chains in a Zif268 mutant highlights the complexities of zinc finger-DNA recognition J. Mol. Biol. 313 2001 309 315
-
(2001)
J. Mol. Biol.
, vol.313
, pp. 309-315
-
-
Miller, J.C.1
Pabo, C.O.2
-
13
-
-
0032981699
-
Toward controlling gene expression at will: Selection and design of zinc finger domains recognizing each of the 5′-GNN-3′ DNA target sequences
-
D.J. Segal, B. Dreier, R.R. Beerli, and C.F. Barbas III Toward controlling gene expression at will: selection and design of zinc finger domains recognizing each of the 5′-GNN-3′ DNA target sequences Proc. Natl Acad. Sci. USA 96 1999 2758 2763
-
(1999)
Proc. Natl Acad. Sci. USA
, vol.96
, pp. 2758-2763
-
-
Segal, D.J.1
Dreier, B.2
Beerli, R.R.3
Barbas III, C.F.4
-
14
-
-
0035800769
-
Development of zinc finger domains for recognition of the 5′-ANN-3′ family of DNA sequences and their use in the construction of artificial transcription factors
-
B. Dreier, R.R. Beerli, D.J. Segal, J.D. Flippin, and C.F. Barbas III Development of zinc finger domains for recognition of the 5′-ANN-3′ family of DNA sequences and their use in the construction of artificial transcription factors J. Biol. Chem. 276 2001 29466 29478
-
(2001)
J. Biol. Chem.
, vol.276
, pp. 29466-29478
-
-
Dreier, B.1
Beerli, R.R.2
Segal, D.J.3
Flippin, J.D.4
Barbas III, C.F.5
-
15
-
-
0036074510
-
Protein-DNA interactions: Amino acid conservation and the effects of mutations on binding specificity
-
N.M. Luscombe, and J.M. Thornton Protein-DNA interactions: amino acid conservation and the effects of mutations on binding specificity J. Mol. Biol. 320 2002 991 1009
-
(2002)
J. Mol. Biol.
, vol.320
, pp. 991-1009
-
-
Luscombe, N.M.1
Thornton, J.M.2
-
16
-
-
0022386929
-
Changing the binding specificity of a repressor by redesigning an alpha-helix
-
R.P. Wharton, and M. Ptashne Changing the binding specificity of a repressor by redesigning an alpha-helix Nature 316 1985 601 605
-
(1985)
Nature
, vol.316
, pp. 601-605
-
-
Wharton, R.P.1
Ptashne, M.2
-
17
-
-
0021130173
-
Substituting an alpha-helix switches the sequence-specific DNA interactions of a repressor
-
R.P. Wharton, E.L. Brown, and M. Ptashne Substituting an alpha-helix switches the sequence-specific DNA interactions of a repressor Cell 38 1984 361 369
-
(1984)
Cell
, vol.38
, pp. 361-369
-
-
Wharton, R.P.1
Brown, E.L.2
Ptashne, M.3
-
18
-
-
0034870112
-
An iteron-related domain is associated to Motif 1 in the replication proteins of geminiviruses: Identification of potential interacting amino acid-base pairs by a comparative approach
-
G.R. Arguello-Astorga, and R. Ruiz-Medrano An iteron-related domain is associated to Motif 1 in the replication proteins of geminiviruses: identification of potential interacting amino acid-base pairs by a comparative approach Arch. Virol. 146 2001 1465 1485
-
(2001)
Arch. Virol.
, vol.146
, pp. 1465-1485
-
-
Arguello-Astorga, G.R.1
Ruiz-Medrano, R.2
-
19
-
-
9644268153
-
Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays
-
S. Mukherjee, M.F. Berger, G. Jona, X.S. Wang, D. Muzzey, and M. Snyder Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays Nature Genet. 36 2004 1331 1339
-
(2004)
Nature Genet.
, vol.36
, pp. 1331-1339
-
-
Mukherjee, S.1
Berger, M.F.2
Jona, G.3
Wang, X.S.4
Muzzey, D.5
Snyder, M.6
-
21
-
-
0035912721
-
Exploring the DNA-binding specificities of zinc fingers with DNA microarrays
-
M.L. Bulyk, X. Huang, Y. Choo, and G.M. Church Exploring the DNA-binding specificities of zinc fingers with DNA microarrays Proc. Natl Acad. Sci. USA 98 2001 7158 7163
-
(2001)
Proc. Natl Acad. Sci. USA
, vol.98
, pp. 7158-7163
-
-
Bulyk, M.L.1
Huang, X.2
Choo, Y.3
Church, G.M.4
-
22
-
-
0742306815
-
Computational prediction of transcription-factor binding site locations
-
M.L. Bulyk Computational prediction of transcription-factor binding site locations Genome Biol. 5 2003 201
-
(2003)
Genome Biol.
, vol.5
, pp. 201
-
-
Bulyk, M.L.1
-
23
-
-
0034538485
-
A comparative study of the immunity region of lambdoid phages including Shiga-toxin-converting phages: Molecular basis for cross immunity
-
K.R. Fattah, S. Mizutani, F.J. Fattah, A. Matsushiro, and Y. Sugino A comparative study of the immunity region of lambdoid phages including Shiga-toxin-converting phages: molecular basis for cross immunity Genes Genet. Syst. 75 2000 223 232
-
(2000)
Genes Genet. Syst.
, vol.75
, pp. 223-232
-
-
Fattah, K.R.1
Mizutani, S.2
Fattah, F.J.3
Matsushiro, A.4
Sugino, Y.5
-
24
-
-
0037825641
-
Prophages and bacterial genomics: What have we learned so far?
-
S. Casjens Prophages and bacterial genomics: what have we learned so far? Mol. Microbiol. 49 2003 277 300
-
(2003)
Mol. Microbiol.
, vol.49
, pp. 277-300
-
-
Casjens, S.1
-
25
-
-
0032479329
-
Crystal structure of lambda-Cro bound to a consensus operator at 3.0 Å resolution
-
R.A. Albright, and B.W. Matthews Crystal structure of lambda-Cro bound to a consensus operator at 3.0 Å resolution J. Mol. Biol. 280 1998 137 151
-
(1998)
J. Mol. Biol.
, vol.280
, pp. 137-151
-
-
Albright, R.A.1
Matthews, B.W.2
-
26
-
-
1842607238
-
Secondary structure switching in Cro protein evolution
-
T. Newlove, J.H. Konieczka, and M.H. Cordes Secondary structure switching in Cro protein evolution Structure (Camb.) 12 2004 569 581
-
(2004)
Structure (Camb.)
, vol.12
, pp. 569-581
-
-
Newlove, T.1
Konieczka, J.H.2
Cordes, M.H.3
-
27
-
-
0020616785
-
Many gene-regulatory proteins appear to have a similar alpha-helical fold that binds DNA and evolved from a common precursor
-
D.H. Ohlendorf, W.F. Anderson, and B.W. Matthews Many gene-regulatory proteins appear to have a similar alpha-helical fold that binds DNA and evolved from a common precursor J. Mol. Evol. 19 1983 109 114
-
(1983)
J. Mol. Evol.
, vol.19
, pp. 109-114
-
-
Ohlendorf, D.H.1
Anderson, W.F.2
Matthews, B.W.3
-
28
-
-
0023779778
-
Transcriptional regulation of early functions of bacteriophage phi 80
-
T. Ogawa, H. Masukata, and J. Tomizawa Transcriptional regulation of early functions of bacteriophage phi 80 J. Mol. Biol. 202 1988 551 563
-
(1988)
J. Mol. Biol.
, vol.202
, pp. 551-563
-
-
Ogawa, T.1
Masukata, H.2
Tomizawa, J.3
-
30
-
-
0029976391
-
Characterization of the primary immunity region of the Escherichia coli linear plasmid prophage N15
-
M.B. Lobocka, A.N. Svarchevsky, V.N. Rybchin, and M.B. Yarmolinsky Characterization of the primary immunity region of the Escherichia coli linear plasmid prophage N15 J. Bacteriol. 178 1996 2902 2910
-
(1996)
J. Bacteriol.
, vol.178
, pp. 2902-2910
-
-
Lobocka, M.B.1
Svarchevsky, A.N.2
Rybchin, V.N.3
Yarmolinsky, M.B.4
-
31
-
-
0016821121
-
Recognition sequences of repressor and polymerase in the operators of bacteriophage lambda
-
T. Maniatis, M. Ptashne, K. Backman, D. Kield, S. Flashman, and A. Jeffrey Recognition sequences of repressor and polymerase in the operators of bacteriophage lambda Cell 5 1975 109 113
-
(1975)
Cell
, vol.5
, pp. 109-113
-
-
Maniatis, T.1
Ptashne, M.2
Backman, K.3
Kield, D.4
Flashman, S.5
Jeffrey, A.6
-
32
-
-
0030986340
-
Overexpression, purification, and analysis of the c1 repressor protein of Pseudomonas aeruginosa bacteriophage D3
-
M.A. Farinha, and A.M. Kropinski Overexpression, purification, and analysis of the c1 repressor protein of Pseudomonas aeruginosa bacteriophage D3 Can. J. Microbiol. 43 1997 220 226
-
(1997)
Can. J. Microbiol.
, vol.43
, pp. 220-226
-
-
Farinha, M.A.1
Kropinski, A.M.2
-
33
-
-
0027173716
-
Highly cooperative DNA binding by the coliphage HK022 repressor
-
N.G. Carlson, and J.W. Little Highly cooperative DNA binding by the coliphage HK022 repressor J. Mol. Biol. 230 1993 1108 1130
-
(1993)
J. Mol. Biol.
, vol.230
, pp. 1108-1130
-
-
Carlson, N.G.1
Little, J.W.2
-
34
-
-
0020475432
-
Control of transcription by the bacteriophage P22 repressor
-
A.R. Poteete, and M. Ptashne Control of transcription by the bacteriophage P22 repressor J. Mol. Biol. 157 1982 21 48
-
(1982)
J. Mol. Biol.
, vol.157
, pp. 21-48
-
-
Poteete, A.R.1
Ptashne, M.2
-
35
-
-
0023048289
-
Bacteriophage P22 Cro protein: Sequence, purification, and properties
-
A.R. Poteete, K. Hehir, and R.T. Sauer Bacteriophage P22 Cro protein: sequence, purification, and properties Biochemistry 25 1986 251 256
-
(1986)
Biochemistry
, vol.25
, pp. 251-256
-
-
Poteete, A.R.1
Hehir, K.2
Sauer, R.T.3
-
36
-
-
0007208716
-
Interactions between DNA-bound repressors govern regulation by the lambda phage repressor
-
A.D. Johnson, B.J. Meyer, and M. Ptashne Interactions between DNA-bound repressors govern regulation by the lambda phage repressor Proc. Natl Acad. Sci. USA 76 1979 5061 5065
-
(1979)
Proc. Natl Acad. Sci. USA
, vol.76
, pp. 5061-5065
-
-
Johnson, A.D.1
Meyer, B.J.2
Ptashne, M.3
-
38
-
-
0034072450
-
DNA binding sites: Representation and discovery
-
G.D. Stormo DNA binding sites: representation and discovery Bioinformatics 16 2000 16 23
-
(2000)
Bioinformatics
, vol.16
, pp. 16-23
-
-
Stormo, G.D.1
-
39
-
-
0035253676
-
Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes
-
L. McCue, W. Thompson, C. Carmack, M.P. Ryan, J.S. Liu, and V. Derbyshire Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes Nucl. Acids Res. 29 2001 774 782
-
(2001)
Nucl. Acids Res.
, vol.29
, pp. 774-782
-
-
McCue, L.1
Thompson, W.2
Carmack, C.3
Ryan, M.P.4
Liu, J.S.5
Derbyshire, V.6
-
40
-
-
0028121003
-
Cooperative DNA-protein interactions. Effects of changing the spacing between adjacent binding sites
-
C. Mao, N.G. Carlson, and J.W. Little Cooperative DNA-protein interactions. Effects of changing the spacing between adjacent binding sites J. Mol. Biol. 235 1994 532 544
-
(1994)
J. Mol. Biol.
, vol.235
, pp. 532-544
-
-
Mao, C.1
Carlson, N.G.2
Little, J.W.3
-
41
-
-
0025008168
-
Sequence logos: A new way to display consensus sequences
-
T.D. Schneider, and R.M. Stephens Sequence logos: a new way to display consensus sequences Nucl. Acids Res. 18 1990 6097 6100
-
(1990)
Nucl. Acids Res.
, vol.18
, pp. 6097-6100
-
-
Schneider, T.D.1
Stephens, R.M.2
-
42
-
-
0024284650
-
Recognition of a DNA operator by the repressor of phage 434: A view at high resolution
-
A.K. Aggarwal, D.W. Rodgers, M. Drottar, M. Ptashne, and S.C. Harrison Recognition of a DNA operator by the repressor of phage 434: a view at high resolution Science 242 1988 899 907
-
(1988)
Science
, vol.242
, pp. 899-907
-
-
Aggarwal, A.K.1
Rodgers, D.W.2
Drottar, M.3
Ptashne, M.4
Harrison, S.C.5
-
43
-
-
0027337534
-
The phage 434 OR2/R1-69 complex at 2.5 Å resolution
-
L.J. Shimon, and S.C. Harrison The phage 434 OR2/R1-69 complex at 2.5 Å resolution J. Mol. Biol. 232 1993 826 838
-
(1993)
J. Mol. Biol.
, vol.232
, pp. 826-838
-
-
Shimon, L.J.1
Harrison, S.C.2
-
44
-
-
0027918646
-
The complex between phage 434 repressor DNA-binding domain and operator site OR3: Structural differences between consensus and non-consensus half-sites
-
D.W. Rodgers, and S.C. Harrison The complex between phage 434 repressor DNA-binding domain and operator site OR3: structural differences between consensus and non-consensus half-sites Structure 1 1993 227 240
-
(1993)
Structure
, vol.1
, pp. 227-240
-
-
Rodgers, D.W.1
Harrison, S.C.2
-
45
-
-
0026657433
-
Refined 1.8 Å crystal structure of the lambda repressor-operator complex
-
L.J. Beamer, and C.O. Pabo Refined 1.8 Å crystal structure of the lambda repressor-operator complex J. Mol. Biol. 227 1992 177 196
-
(1992)
J. Mol. Biol.
, vol.227
, pp. 177-196
-
-
Beamer, L.J.1
Pabo, C.O.2
-
46
-
-
0032584223
-
How Cro and lambda-repressor distinguish between operators: The structural basis underlying a genetic switch
-
R.A. Albright, and B.W. Matthews How Cro and lambda-repressor distinguish between operators: the structural basis underlying a genetic switch Proc. Natl Acad. Sci. USA 95 1998 3431 3436
-
(1998)
Proc. Natl Acad. Sci. USA
, vol.95
, pp. 3431-3436
-
-
Albright, R.A.1
Matthews, B.W.2
-
47
-
-
0025320805
-
An expectation maximization (EM) algorithm for the identification and characterization of common sites in unaligned biopolymer sequences
-
C.E. Lawrence, and A.A. Reilly An expectation maximization (EM) algorithm for the identification and characterization of common sites in unaligned biopolymer sequences Proteins: Struct. Funct. Genet. 7 1990 41 51
-
(1990)
Proteins: Struct. Funct. Genet.
, vol.7
, pp. 41-51
-
-
Lawrence, C.E.1
Reilly, A.A.2
-
48
-
-
0030595337
-
Structural classification of HTH DNA-binding domains and protein-DNA interaction modes
-
R. Wintjens, and M. Rooman Structural classification of HTH DNA-binding domains and protein-DNA interaction modes J. Mol. Biol. 262 1996 294 313
-
(1996)
J. Mol. Biol.
, vol.262
, pp. 294-313
-
-
Wintjens, R.1
Rooman, M.2
-
49
-
-
0029018450
-
DNA recognition and superstructure formation by helix-turn-helix proteins
-
M. Suzuki, N. Yagi, and M. Gerstein DNA recognition and superstructure formation by helix-turn-helix proteins Protein Eng. 8 1995 329 338
-
(1995)
Protein Eng.
, vol.8
, pp. 329-338
-
-
Suzuki, M.1
Yagi, N.2
Gerstein, M.3
-
50
-
-
0026645262
-
Lac repressor with the helix-turn-helix motif of lambda cro binds to lac operator
-
P. Kolkhof, D. Teichmann, B. Kisters-Woike, B. von Wilcken-Bergmann, and B. Muller-Hill Lac repressor with the helix-turn-helix motif of lambda cro binds to lac operator EMBO J. 11 1992 3031 3038
-
(1992)
EMBO J.
, vol.11
, pp. 3031-3038
-
-
Kolkhof, P.1
Teichmann, D.2
Kisters-Woike, B.3
Von Wilcken-Bergmann, B.4
Muller-Hill, B.5
-
51
-
-
0030969635
-
Combinations of the alpha-helix-turn-alpha-helix motif of TetR with respective residues from LacI or 434 Cro: DNA recognition, inducer binding, and urea-dependent denaturation
-
H. Backes, C. Berens, V. Helbl, S. Walter, F.X. Schmid, and W. Hillen Combinations of the alpha-helix-turn-alpha-helix motif of TetR with respective residues from LacI or 434 Cro: DNA recognition, inducer binding, and urea-dependent denaturation Biochemistry 36 1997 5311 5322
-
(1997)
Biochemistry
, vol.36
, pp. 5311-5322
-
-
Backes, H.1
Berens, C.2
Helbl, V.3
Walter, S.4
Schmid, F.X.5
Hillen, W.6
-
52
-
-
0028609064
-
DNA recognition code of transcription factors in the helix-turn-helix, probe helix, hormone receptor, and zinc finger families
-
M. Suzuki, and N. Yagi DNA recognition code of transcription factors in the helix-turn-helix, probe helix, hormone receptor, and zinc finger families Proc. Natl Acad. Sci. USA 91 1994 12357 12361
-
(1994)
Proc. Natl Acad. Sci. USA
, vol.91
, pp. 12357-12361
-
-
Suzuki, M.1
Yagi, N.2
-
53
-
-
0031574072
-
The CLUSTAL_X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools
-
J.D. Thompson, T.J. Gibson, F. Plewniak, F. Jeanmougin, and D.G. Higgins The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools Nucl. Acids Res. 25 1997 4876 4882
-
(1997)
Nucl. Acids Res.
, vol.25
, pp. 4876-4882
-
-
Thompson, J.D.1
Gibson, T.J.2
Plewniak, F.3
Jeanmougin, F.4
Higgins, D.G.5
-
54
-
-
0026244229
-
MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures
-
P.J. Kraulis MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures J. Appl. Crystallog. 24 1991 946 950
-
(1991)
J. Appl. Crystallog.
, vol.24
, pp. 946-950
-
-
Kraulis, P.J.1
-
55
-
-
0030815133
-
Raster3D: Photorealistic molecular graphics
-
E.A. Merritt, and D.J. Bacon Raster3D: photorealistic molecular graphics Methods Enzymol. 277 1997 505 524
-
(1997)
Methods Enzymol.
, vol.277
, pp. 505-524
-
-
Merritt, E.A.1
Bacon, D.J.2
|