-
1
-
-
0001972983
-
The DNA helix and how it is read
-
Dickerson, R.E. (1983) The DNA helix and how it is read. Sci. Am., 249, 94-111.
-
(1983)
Sci. Am.
, vol.249
, pp. 94-111
-
-
Dickerson, R.E.1
-
2
-
-
20544460658
-
Protein-DNA recognition patterns and predictions
-
Sarai, A. and Kono, H. (2005) Protein-DNA recognition patterns and predictions. Annu. Rev. Biophys. Biomol. Struct., 34, 379-398.
-
(2005)
Annu. Rev. Biophys. Biomol. Struct.
, vol.34
, pp. 379-398
-
-
Sarai, A.1
Kono, H.2
-
3
-
-
0036086459
-
The Papillomavirus E2 proteins: structure, function, and biology
-
Hegde, R.S. (2002) The Papillomavirus E2 proteins: structure, function, and biology. Annu. Rev. Biophys. Biomol. Struct., 31, 343-360.
-
(2002)
Annu. Rev. Biophys. Biomol. Struct.
, vol.31
, pp. 343-360
-
-
Hegde, R.S.1
-
4
-
-
0036143789
-
Sequence selectivity and degeneracy of a restriction endonuclease mediated by DNA intercalation
-
Horton, N.C., Dorner, L.F. and Perona, J.J. (2002) Sequence selectivity and degeneracy of a restriction endonuclease mediated by DNA intercalation. Nature Struct. Biol., 9, 42-47.
-
(2002)
Nature Struct. Biol.
, vol.9
, pp. 42-47
-
-
Horton, N.C.1
Dorner, L.F.2
Perona, J.J.3
-
5
-
-
0032518220
-
Recognition of DNA structure by 434 repressor
-
Koudelka, G.B. (1998) Recognition of DNA structure by 434 repressor. Nucleic Acids Res., 26, 669-675.
-
(1998)
Nucleic Acids Res.
, vol.26
, pp. 669-675
-
-
Koudelka, G.B.1
-
6
-
-
0346996697
-
Recognition of '-YpG-3' sequences by coupled stacking/hydrogen bonding interactions with amino acid residues
-
Lamoureux, J.S., Maynes, J.T. and Mark Glover, J.N. (2004) Recognition of 5′-YpG-3' sequences by coupled stacking/hydrogen bonding interactions with amino acid residues. J. Mol. Biol., 335, 399-408.
-
(2004)
J. Mol. Biol.
, vol.335
, pp. 399-408
-
-
Lamoureux, J.S.1
Maynes, J.T.2
Mark Glover, J.N.3
-
7
-
-
1342345189
-
Catabolite activator protein: DNA binding and transcription activation
-
Lawson, C.L., Swigon, D., Murakami, K.S., Darst, S.A., Berman, H.M. and Ebright, R.H. (2004) Catabolite activator protein: DNA binding and transcription activation. Curr. Opin. Struct. Biol., 14, 10-20.
-
(2004)
Curr. Opin. Struct. Biol.
, vol.14
, pp. 10-20
-
-
Lawson, C.L.1
Swigon, D.2
Murakami, K.S.3
Darst, S.A.4
Berman, H.M.5
Ebright, R.H.6
-
8
-
-
0032530555
-
DNA sequence-dependent deformability deduced from protein-DNA crystal complexes
-
Olson, W.K., Gorin, A.A., Lu, X.J., Hock, L.M. and Zhurkin, V.B. (1998) DNA sequence-dependent deformability deduced from protein-DNA crystal complexes. Proc. Natl Acad. Sci. USA, 95, 11163-11168.
-
(1998)
Proc. Natl Acad. Sci. USA
, vol.95
, pp. 11163-11168
-
-
Olson, W.K.1
Gorin, A.A.2
Lu, X.J.3
Hock, L.M.4
Zhurkin, V.B.5
-
9
-
-
0038226895
-
DNA sequence and structure: direct and indirect recognition in protein-DNA binding
-
Steffen, N.R., Murphy, S.D., Tolleri, L., Hatfield, G.W. and Lathrop, R.H. (2002) DNA sequence and structure: direct and indirect recognition in protein-DNA binding. Bioinformatics, 18(Suppl. 1), S22-S30.
-
(2002)
Bioinformatics
, vol.18
, Issue.SUPPL. 1
-
-
Steffen, N.R.1
Murphy, S.D.2
Tolleri, L.3
Hatfield, G.W.4
Lathrop, R.H.5
-
10
-
-
0242290881
-
DNA basepair step deformability inferred from molecular dynamics simulations
-
Lankaš, F., Šponer, J., Langowski, J. and Cheatham, T.E. III. (2003) DNA basepair step deformability inferred from molecular dynamics simulations. Biophys. J., 85, 2872-2883.
-
(2003)
Biophys. J.
, vol.85
, pp. 2872-2883
-
-
Lankaš, F.1
Šponer, J.2
Langowski, J.3
Cheatham T.E. III4
-
11
-
-
1442323773
-
Intermolecular and intramolecular readout mechanisms in protein-DNA recognition
-
Gromiha, M.M., Siebers, J.G., Selvaraj, S., Kono, H. and Sarai, A. (2004) Intermolecular and intramolecular readout mechanisms in protein-DNA recognition. J. Mol. Biol., 337, 285-294.
-
(2004)
J. Mol. Biol.
, vol.337
, pp. 285-294
-
-
Gromiha, M.M.1
Siebers, J.G.2
Selvaraj, S.3
Kono, H.4
Sarai, A.5
-
12
-
-
28844509776
-
Role of inter and intramolecular interactions in protein-DNA recognition
-
Gromiha, M.M., Slebcrs, J.G., Selvaraj, S., Kono, H. and Sarai, A. (2005) Role of inter and intramolecular interactions in protein-DNA recognition. Gene, 364, 108-113.
-
(2005)
Gene
, vol.364
, pp. 108-113
-
-
Gromiha, M.M.1
Slebcrs, J.G.2
Selvaraj, S.3
Kono, H.4
Sarai, A.5
-
13
-
-
28044444099
-
Sequence-dependent conformational energy of DNA derived from molecular dynamics simulations: toward understanding the indirect readout mechanism in protein-DNA recognition
-
Araúzo-Bravo, M.J., Fujii, S., Kono, H., Ahmad, S. and Sarai, A. (2005) Sequence-dependent conformational energy of DNA derived from molecular dynamics simulations: toward understanding the indirect readout mechanism in protein-DNA recognition. J. Am. Chem. Soc., 127, 16074-16089.
-
(2005)
J. Am. Chem. Soc.
, vol.127
, pp. 16074-16089
-
-
Araúzo-Bravo, M.J.1
Fujii, S.2
Kono, H.3
Ahmad, S.4
Sarai, A.5
-
14
-
-
33751003527
-
Indirect readout: detection of optimized subsequences and calculation of relative binding affinities using different DNA elastic potentials
-
Becker, N.B., Wolff, L. and Everaers, R. (2006) Indirect readout: detection of optimized subsequences and calculation of relative binding affinities using different DNA elastic potentials. Nucleic Acids Res., 34, 5638-5649.
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. 5638-5649
-
-
Becker, N.B.1
Wolff, L.2
Everaers, R.3
-
15
-
-
35548987996
-
Sequence-dependent DNA deformability studied using molecular dynamics simulations
-
Fujii, S., Kono, H., Takenaka, S., Go, N. and Sarai, A. (2007) Sequence-dependent DNA deformability studied using molecular dynamics simulations. Nucleic Acids Res., 35, 6063-6074.
-
(2007)
Nucleic Acids Res.
, vol.35
, pp. 6063-6074
-
-
Fujii, S.1
Kono, H.2
Takenaka, S.3
Go, N.4
Sarai, A.5
-
16
-
-
1642452665
-
Analyzing protein-DNA recognition mechanisms
-
Paillard, G. and Lavery, R. (2004) Analyzing protein-DNA recognition mechanisms. Structure, 12, 113-122.
-
(2004)
Structure
, vol.12
, pp. 113-122
-
-
Paillard, G.1
Lavery, R.2
-
17
-
-
0035850731
-
A standard reference frame for the description of nucleic acid base-pair geometry
-
Olson, W.K., Bansal, M., Burley, S.K., Dickerson, R.E., Gerstein, M., Harvey, S.C., Heinemann, U., Lu, X.J., Neidle, S., Shakked, Z. et al. (2001) A standard reference frame for the description of nucleic acid base-pair geometry. J. Mol. Biol., 313, 229-237.
-
(2001)
J. Mol. Biol.
, vol.313
, pp. 229-237
-
-
Olson, W.K.1
Bansal, M.2
Burley, S.K.3
Dickerson, R.E.4
Gerstein, M.5
Harvey, S.C.6
Heinemann, U.7
Lu, X.J.8
Neidle, S.9
Shakked, Z.10
-
18
-
-
0042386600
-
Sequence-dependent DNA structure: a database of octamer structural parameters
-
Gardiner, E.J., Hunter, C.A., Packer, M.J., Palmer, D.S. and Willett, P. (2003) Sequence-dependent DNA structure: a database of octamer structural parameters. J. Mol. Biol., 332, 1025-1035.
-
(2003)
J. Mol. Biol.
, vol.332
, pp. 1025-1035
-
-
Gardiner, E.J.1
Hunter, C.A.2
Packer, M.J.3
Palmer, D.S.4
Willett, P.5
-
19
-
-
0034614483
-
Sequence-dependent DNA structure: dinucleotide conformational maps
-
Packer, M.J., Dauncey, M.P. and Hunter, C.A. (2000) Sequence-dependent DNA structure: dinucleotide conformational maps. J. Mol. Biol., 295, 71-83.
-
(2000)
J. Mol. Biol.
, vol.295
, pp. 71-83
-
-
Packer, M.J.1
Dauncey, M.P.2
Hunter, C.A.3
-
20
-
-
0034614487
-
Sequence-dependent DNA structure: tetranucleotide conformational maps
-
Packer, M.J., Dauncey, M.P. and Hunter, C.A. (2000) Sequence-dependent DNA structure: tetranucleotide conformational maps. J. Mol. Biol., 295, 85-103.
-
(2000)
J. Mol. Biol.
, vol.295
, pp. 85-103
-
-
Packer, M.J.1
Dauncey, M.P.2
Hunter, C.A.3
-
21
-
-
0242396923
-
3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures
-
Lu, X.J. and Olson, W.K. (2003) 3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. Nucleic Acids Res., 31, 5108-5121.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 5108-5121
-
-
Lu, X.J.1
Olson, W.K.2
-
22
-
-
0026742978
-
The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids
-
Berman, H.M., Olson, W.K., Beveridge, D.L., Westbrook, J., Gelbin, A., Demeny, T., Hsieh, S.H., Srinivasan, A.R. and Schneider, B. (1992) The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids. Biophys. J., 63, 751-759.
-
(1992)
Biophys. J.
, vol.63
, pp. 751-759
-
-
Berman, H.M.1
Olson, W.K.2
Beveridge, D.L.3
Westbrook, J.4
Gelbin, A.5
Demeny, T.6
Hsieh, S.H.7
Srinivasan, A.R.8
Schneider, B.9
-
23
-
-
4043179941
-
DNA and its counterions: a molecular dynamics study
-
Varnai, P. and Zakrzewska, K. (2004) DNA and its counterions: a molecular dynamics study. Nucleic Acids Res., 32, 4269-4280.
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. 4269-4280
-
-
Varnai, P.1
Zakrzewska, K.2
-
24
-
-
0034864528
-
Generalized-ensemble algorithms for molecular simulations of biopolymers
-
Mitsutake, A., Sugita, Y. and Okamoto, Y. (2001) Generalized-ensemble algorithms for molecular simulations of biopolymers. Biopolymers (Pept. Sci.), 60, 96-123.
-
(2001)
Biopolymers (Pept. Sci.)
, vol.60
, pp. 96-123
-
-
Mitsutake, A.1
Sugita, Y.2
Okamoto, Y.3
-
25
-
-
34250318638
-
Refinement of the AMBER force field for nucleic acids: improving the description of α/γ conformers
-
Perez, A., Marchan, I., Svozil, D., Sponer, J., Cheatham, T.E. III, Laughton, C.A. and Orozco, M. (2007) Refinement of the AMBER force field for nucleic acids: improving the description of α/γ conformers. Biophys. J., 92, 3817-3829.
-
(2007)
Biophys. J.
, vol.92
, pp. 3817-3829
-
-
Perez, A.1
Marchan, I.2
Svozil, D.3
Sponer, J.4
Cheatham T.E. III5
Laughton, C.A.6
Orozco, M.7
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