-
1
-
-
0033647653
-
An overview of the structures of protein-DNA complexes
-
REVIEWS001
-
Luscombe,N.M., Austin,S.E., Berman,H.M. and Thornton,J.M. (2000) An overview of the structures of protein-DNA complexes. Genome Biol., 1, REVIEWS001.
-
(2000)
Genome Biol.
, vol.1
-
-
Luscombe, N.M.1
Austin, S.E.2
Berman, H.M.3
Thornton, J.M.4
-
2
-
-
0036220597
-
Mining genome databases to identify and understand new gene regulatory systems
-
Stormo,G.D. and Tan,K. (2002) Mining genome databases to identify and understand new gene regulatory systems. Curr. Opin. Microbiol., 5, 149-153.
-
(2002)
Curr. Opin. Microbiol.
, vol.5
, pp. 149-153
-
-
Stormo, G.D.1
Tan, K.2
-
3
-
-
0035232321
-
One-hybrid systems for detecting protein-DNA interactions
-
Alexander,M.K., Bourns,B.D. and Zakian,V.A. (2001) One-hybrid systems for detecting protein-DNA interactions. Methods Mol. Biol., 177, 241-59.
-
(2001)
Methods Mol. Biol.
, vol.177
, pp. 241-259
-
-
Alexander, M.K.1
Bourns, B.D.2
Zakian, V.A.3
-
4
-
-
0034704248
-
Genome-wide location and function of DNA binding proteins
-
Ren,B., Robert,F., Wyrick,J.J., Aparicio,O., Jennings,E.G., Simon.I., Zeitlinger,J., Schreiber,J., Hannett,N., Kanin,E., Volkert,T.L., Wilson,C.J., Bell,S.P. and Young,R.A. (2000) Genome-wide location and function of DNA binding proteins. Science. 290, 2306-2309.
-
(2000)
Science
, vol.290
, pp. 2306-2309
-
-
Ren, B.1
Robert, F.2
Wyrick, J.J.3
Aparicio, O.4
Jennings, E.G.5
Simon, I.6
Zeitlinger, J.7
Schreiber, J.8
Hannett, N.9
Kanin, E.10
Volkert, T.L.11
Wilson, C.J.12
Bell, S.P.13
Young, R.A.14
-
5
-
-
0036022523
-
High-throughput SELEX SAGE method for quantitative modeling of transcription-factor binding sites
-
Roulet,E., Busso,S., Camargo,A.A., Simpson,A.J., Mermod,N. and Bucher,P. (2002) High-throughput SELEX SAGE method for quantitative modeling of transcription-factor binding sites. Nat. Biotechnol., 20, 831-835.
-
(2002)
Nat. Biotechnol.
, vol.20
, pp. 831-835
-
-
Roulet, E.1
Busso, S.2
Camargo, A.A.3
Simpson, A.J.4
Mermod, N.5
Bucher, P.6
-
6
-
-
0035912721
-
Exploring the DNA-binding specificities of zinc fingers with DNA microarrays
-
Bulyk,M.L., Huang,X., Choo,Y., Church,G.M. (2001) Exploring the DNA-binding specificities of zinc fingers with DNA microarrays. Proc. Natl Acad. Sci. USA, 98, 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
-
7
-
-
0036013781
-
Is there a code for protein-DNA recognition? Probab(ilistical)ly
-
Benos,P.V., Lapedes,A.S. and Stormo,G.D. (2002) Is there a code for protein-DNA recognition? Probab(ilistical)ly. Bioessays, 24, 466-475.
-
(2002)
Bioessays
, vol.24
, pp. 466-475
-
-
Benos, P.V.1
Lapedes, A.S.2
Stormo, G.D.3
-
8
-
-
0024294636
-
Protein-DNA interaction. No code for recognition
-
Matthews,B.W. (1988) Protein-DNA interaction. No code for recognition. Nature, 335, 294-295.
-
(1988)
Nature
, vol.335
, pp. 294-295
-
-
Matthews, B.W.1
-
9
-
-
0031042082
-
Physical basis of a protein-DNA recognition code
-
Choo,Y. and Klug,A. (1997) Physical basis of a protein-DNA recognition code. Curr. Opin. Struct. Biol., 7, 117-125.
-
(1997)
Curr. Opin. Struct. Biol.
, vol.7
, pp. 117-125
-
-
Choo, Y.1
Klug, A.2
-
10
-
-
0033524954
-
Analysis of zinc fingers optimized via phage display: Evaluating the utility of a recognition code
-
Wolfe,S.A., Greisman,H.A., Ramm,E.I. and Pabo,C.O. (1999) Analysis of zinc fingers optimized via phage display: evaluating the utility of a recognition code. J. Mol. Biol., 285, 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
-
11
-
-
0032524713
-
Quantitative parameters for amino acid-base interaction: Implications for prediction of protein-DNA binding sites
-
Mandel-Gutfreund,Y. and Margalit,H. (1998) Quantitative parameters for amino acid-base interaction: implications for prediction of protein-DNA binding sites. Nucleic Acids Rev., 26, 2306-2312.
-
(1998)
Nucleic Acids Rev.
, vol.26
, pp. 2306-2312
-
-
Mandel-Gutfreund, Y.1
Margalit, H.2
-
12
-
-
0036977044
-
Probabilistic code for DNA recognition by proteins of the EGR family
-
Benos,P.V., Lapedes,A.S. and Stormo.G.D. (2002) Probabilistic code for DNA recognition by proteins of the EGR family. J. Mol. Biol., 323, 701-727.
-
(2002)
J. Mol. Biol.
, vol.323
, pp. 701-727
-
-
Benos, P.V.1
Lapedes, A.S.2
Stormo, G.D.3
-
13
-
-
0029065860
-
DNA recognition code of transcription factors
-
Suzuki,M., Brenner,S.E., Gerstein,M. and Yagi,N. (1995) DNA recognition code of transcription factors. Protein Eng., 8, 319-328.
-
(1995)
Protein Eng.
, vol.8
, pp. 319-328
-
-
Suzuki, M.1
Brenner, S.E.2
Gerstein, M.3
Yagi, N.4
-
14
-
-
0033120215
-
Structure-based prediction of DNA target sites by regulatory proteins
-
Kono,H. and Sarai,A. (1999) Structure-based prediction of DNA target sites by regulatory proteins. Proteins, 35, 114-131.
-
(1999)
Proteins
, vol.35
, pp. 114-131
-
-
Kono, H.1
Sarai, A.2
-
15
-
-
0034072450
-
DNA binding sites: Representation and discovery
-
Stormo,G.D. (2000) DNA binding sites: representation and discovery. Bioinformatics, 16, 16-23.
-
(2000)
Bioinformatics
, vol.16
, pp. 16-23
-
-
Stormo, G.D.1
-
16
-
-
0035875327
-
Non-independence of Mnt repressor-operator interaction determined by a new Quantitative Multiple Fluorescence Relative Affinity (QuMFRA) assay
-
Man,T.-K. and Stormo,G.D. (2001) Non-independence of Mnt repressor-operator interaction determined by a new Quantitative Multiple Fluorescence Relative Affinity (QuMFRA) assay. Nucleic Acids Res., 29, 2471-2478.
-
(2001)
Nucleic Acids Res.
, vol.29
, pp. 2471-2478
-
-
Man, T.-K.1
Stormo, G.D.2
-
17
-
-
0036493201
-
Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors
-
Bulyk,M., Johnson,P.L. and Church,G.M. (2002) Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors. Nucleic Acids Rev., 30, 1255-1261.
-
(2002)
Nucleic Acids Rev.
, vol.30
, pp. 1255-1261
-
-
Bulyk, M.1
Johnson, P.L.2
Church, G.M.3
-
18
-
-
0037109192
-
Additivity in protein-DNA interactions: How good an approximation is it?
-
Benos,P.V., Bulyk.M.L. and Stormo,G.D. (2002) Additivity in protein-DNA interactions: how good an approximation is it? Nucleic Acids Res., 30, 4442-4451.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 4442-4451
-
-
Benos, P.V.1
Bulyk, M.L.2
Stormo, G.D.3
-
19
-
-
0027211894
-
Additivity of mutant effects assessed by binomial mutagenesis
-
Gregoret,L.M. and Sauer,R.T. (1993) Additivity of mutant effects assessed by binomial mutagenesis. Proc. Natl Acad. Sci. USA, 90, 4246-4250.
-
(1993)
Proc. Natl. Acad. Sci. USA
, vol.90
, pp. 4246-4250
-
-
Gregoret, L.M.1
Sauer, R.T.2
-
20
-
-
0028147466
-
Major groove DNA recognition by β-sheets: The ribbon-helix-helix family of gene regulatory proteins
-
Raumann,B.E., Brown,B.M. and Sauer,R.T. (1994) Major groove DNA recognition by β-sheets: the ribbon-helix-helix family of gene regulatory proteins. Curr. Opin. Struct. Biol., 4, 36-43.
-
(1994)
Curr. Opin. Struct. Biol.
, vol.4
, pp. 36-43
-
-
Raumann, B.E.1
Brown, B.M.2
Sauer, R.T.3
-
21
-
-
0021044857
-
Changing the DNA-binding specificity of a repressor
-
Youderian,P., Vershon,A., Bouvier,S., Sauer,R.T., and Susskind,M.M. (1983) Changing the DNA-binding specificity of a repressor. Cell, 35, 777-783.
-
(1983)
Cell
, vol.35
, pp. 777-783
-
-
Youderian, P.1
Vershon, A.2
Bouvier, S.3
Sauer, R.T.4
Susskind, M.M.5
-
22
-
-
0028843773
-
Dramatic changes in DNA-binding specificity caused by single residue substitutions in an Arc/Mnt hybrid repressor
-
Raumann,B.E., Knight,K.L. and Sauer,R.T. (1995) Dramatic changes in DNA-binding specificity caused by single residue substitutions in an Arc/Mnt hybrid repressor. Nature Struct. Biol., 2, 1115-1122.
-
(1995)
Nature Struct. Biol.
, vol.2
, pp. 1115-1122
-
-
Raumann, B.E.1
Knight, K.L.2
Sauer, R.T.3
-
23
-
-
0037115830
-
Specificity of Mnt 'master residue' obtained from in vivo and in vitro selections
-
Silbaq,F.S. Ruttenberg,S.E. and Stormo,G.D. (2002) Specificity of Mnt 'master residue' obtained from in vivo and in vitro selections. Nucleic Acids Res., 30, 5539-5548.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 5539-5548
-
-
Silbaq, F.S.1
Ruttenberg, S.E.2
Stormo, G.D.3
-
24
-
-
0025008168
-
Sequence logos: A new way to display consensus sequences
-
Schneider,T.D. and Stephens,R.M. (1990) Sequence logos: a new way to display consensus sequences. Nucleic Acids Res., 18, 6097-6100.
-
(1990)
Nucleic Acids Res.
, vol.18
, pp. 6097-6100
-
-
Schneider, T.D.1
Stephens, R.M.2
-
25
-
-
0031571660
-
Quantitative specificity of Mnt repressor
-
Fields,D.S., He,Y-Y., Al-Uzri,A.Y. and Stormo,G.D. (1997) Quantitative specificity of Mnt repressor. J. Mol. Biol.. 271, 178-194.
-
(1997)
J. Mol. Biol.
, vol.271
, pp. 178-194
-
-
Fields, D.S.1
He, Y-Y.2
Al-Uzri, A.Y.3
Stormo, G.D.4
-
26
-
-
0032032780
-
Specificity, energy and information in DNA-protein interactions
-
Stormo,G.D. and Fields,D.S. (1998) Specificity, energy and information in DNA-protein interactions. Trends Biochem. Sci., 23, 109-113.
-
(1998)
Trends Biochem. Sci.
, vol.23
, pp. 109-113
-
-
Stormo, G.D.1
Fields, D.S.2
-
27
-
-
0026466830
-
Identifying constraints on the higher-order structure of RNA: Continued development and application of comparative sequence analysis methods
-
Gutell,R.R., Power,A., Hertz,G.Z., Putz,E.J. and Stormo,G.D. (1992) Identifying constraints on the higher-order structure of RNA: continued development and application of comparative sequence analysis methods. Nucleic Acids Res., 20, 5785-57.
-
(1992)
Nucleic Acids Res.
, vol.20
, pp. 5785-6757
-
-
Gutell, R.R.1
Power, A.2
Hertz, G.Z.3
Putz, E.J.4
Stormo, G.D.5
-
28
-
-
0031473030
-
Displaying the information contents of structural RNA alignments: The structure logos
-
Gorodkin,J., Heyer,L.J., Brunak,S. and Stormo,G.D. (1997) Displaying the information contents of structural RNA alignments: the structure logos. Comput. Appl. Biosci., 13, 583-586.
-
(1997)
Comput. Appl. Biosci.
, vol.13
, pp. 583-586
-
-
Gorodkin, J.1
Heyer, L.J.2
Brunak, S.3
Stormo, G.D.4
-
29
-
-
0028177303
-
DNA recognition by beta-sheets in the Arc repressor-operator crystal structure
-
Raumann,B.E., Rould,M.A., Pabo,C.O. and Sauer,R.T. (1994) DNA recognition by beta-sheets in the Arc repressor-operator crystal structure. Nature, 367, 754-757.
-
(1994)
Nature
, vol.367
, pp. 754-757
-
-
Raumann, B.E.1
Rould, M.A.2
Pabo, C.O.3
Sauer, R.T.4
|