-
1
-
-
84950267569
-
Crystallographic databases: Search and retrieval of information from the Cambridge Structural Database
-
J. D. Dunitz, & H.-B. Bürgi. New York: VCH Publisher
-
Allen F. H., Kennard O., Watson D. G. Crystallographic databases: search and retrieval of information from the Cambridge Structural Database. Dunitz J. D., Bürgi H.-B. Structure Correlation. 1994;71-ü110 VCH Publisher, New York.
-
(1994)
Structure Correlation
, pp. 71-110
-
-
Allen, F.H.1
Kennard, O.2
Watson, D.G.3
-
2
-
-
0031776981
-
The structure of PurR mutant L54M shows an alternative route to DNA kinking
-
Arvidson D. N., Lu F., Faber C., Zalkin H., Brennan R. G. The structure of PurR mutant L54M shows an alternative route to DNA kinking. Nature Struct. Biol. 5:1998;436-441.
-
(1998)
Nature Struct. Biol.
, vol.5
, pp. 436-441
-
-
Arvidson, D.N.1
Lu, F.2
Faber, C.3
Zalkin, H.4
Brennan, R.G.5
-
3
-
-
0028221654
-
The effect of mathematics and coordinate system on comparability and "dependencies" of nucleic acid structure parameters
-
Babcock M. S., Olson W. K. The effect of mathematics and coordinate system on comparability and "dependencies" of nucleic acid structure parameters. J. Mol. Biol. 237:1994;98-124.
-
(1994)
J. Mol. Biol.
, vol.237
, pp. 98-124
-
-
Babcock, M.S.1
Olson, W.K.2
-
4
-
-
0028230287
-
Nucleic acid structure analysis: Mathematics for local cartesian and helical structure parameters that are truly comparable between structures
-
Babcock M. S., Pednault E. P. D., Olson W. K. Nucleic acid structure analysis: mathematics for local cartesian and helical structure parameters that are truly comparable between structures. J. Mol. Biol. 237:1994;125-156.
-
(1994)
J. Mol. Biol.
, vol.237
, pp. 125-156
-
-
Babcock, M.S.1
Pednault, E.P.D.2
Olson, W.K.3
-
5
-
-
0029023343
-
NUPARM and NUCGEN: Software for analysis and generation of sequence dependent nucleic acid structures
-
Bansal M., Bhattacharyya D., Ravi B. NUPARM and NUCGEN: software for analysis and generation of sequence dependent nucleic acid structures. Comput. Appl. Biosci. 11:1995;281-287.
-
(1995)
Comput. Appl. Biosci.
, vol.11
, pp. 281-287
-
-
Bansal, M.1
Bhattacharyya, D.2
Ravi, B.3
-
6
-
-
0014413509
-
The interaction of closed circular DNA with intercalative dyes. I. The superhelix density of SV40 DNA in the presence and absence of dye
-
Bauer W., Vinograd J. The interaction of closed circular DNA with intercalative dyes. I. The superhelix density of SV40 DNA in the presence and absence of dye. J. Mol. Biol. 33:1968;141-171.
-
(1968)
J. Mol. Biol.
, vol.33
, pp. 141-171
-
-
Bauer, W.1
Vinograd, J.2
-
7
-
-
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 L., Gelbin A., Demeny T., Hsieh S. H., Srinivasan A. R., Schneider B. The nucleic acid database: a comprehensive relational database of three dimensional structures of nucleic acids. Biophys. J. 63:1992;751-759.
-
(1992)
Biophys. J.
, vol.63
, pp. 751-759
-
-
Berman, H.M.1
Olson, W.K.2
Beveridge, D.L.3
Westbrook, L.4
Gelbin, A.5
Demeny, T.6
Hsieh, S.H.7
Srinivasan, A.R.8
Schneider, B.9
-
8
-
-
0024543897
-
A self-consistent formulation for analysis and generation of non-uniform DNA structures
-
Bhattacharyya D., Bansal M. A self-consistent formulation for analysis and generation of non-uniform DNA structures. J. Biomol. Struct. Dynam. 6:1989;635-653.
-
(1989)
J. Biomol. Struct. Dynam.
, vol.6
, pp. 635-653
-
-
Bhattacharyya, D.1
Bansal, M.2
-
9
-
-
0025648066
-
Local variability and base sequence effects in DNA crystal structure
-
Bhattacharyya D., Bansal M. Local variability and base sequence effects in DNA crystal structure. J. Biomol. Struct. Dynam. 8:1990;539-572.
-
(1990)
J. Biomol. Struct. Dynam.
, vol.8
, pp. 539-572
-
-
Bhattacharyya, D.1
Bansal, M.2
-
10
-
-
0030051966
-
Geometric parameters in nucleic acids: Nitrogenous bases
-
Clowney L., Jain S. C., Srinivasan A. R., Westbrook J., Olson W. K., Berman H. M. Geometric parameters in nucleic acids: nitrogenous bases. J. Am. Chem. Soc. 118:1996;509-518.
-
(1996)
J. Am. Chem. Soc.
, vol.118
, pp. 509-518
-
-
Clowney, L.1
Jain, S.C.2
Srinivasan, A.R.3
Westbrook, J.4
Olson, W.K.5
Berman, H.M.6
-
11
-
-
0342565151
-
Helix comparison table
-
F. A. Jurnak, & A. McPherson. New York: Wiley-Interscience
-
Dickerson R. E. Helix comparison table. Jurnak F. A., McPherson A. Biological Macromolecules and Assemblies. 1985;471-494 Wiley-Interscience, New York.
-
(1985)
Biological Macromolecules and Assemblies
, pp. 471-494
-
-
Dickerson, R.E.1
-
12
-
-
0032522139
-
DNA bending: The prevalence of kinkiness and the virtues of normality
-
Dickerson R. E. DNA bending: the prevalence of kinkiness and the virtues of normality. Nucl. Acids Res. 26:1998;1906-1926.
-
(1998)
Nucl. Acids Res.
, vol.26
, pp. 1906-1926
-
-
Dickerson, R.E.1
-
13
-
-
0024974308
-
Definitions and nomenclature of nucleic acid structure parameters
-
Dickerson R. E., Bansal M., Calladine C. R., Diekmann S., Hunter W. N., Kennard O., Lavery R., Nelson H. C. M., Olson W. A., Saenger W., Shakked Z., Sklenar H., Soumpasis D. M., Tung C.-S., von Kitzing E. et al. Definitions and nomenclature of nucleic acid structure parameters. J. Mol. Biol. 205:1989;787-791.
-
(1989)
J. Mol. Biol.
, vol.205
, pp. 787-791
-
-
Dickerson, R.E.1
Bansal, M.2
Calladine, C.R.3
Diekmann, S.4
Hunter, W.N.5
Kennard, O.6
Lavery, R.7
Nelson, H.C.M.8
Olson, W.A.9
Saenger, W.10
Shakked, Z.11
Sklenar, H.12
Soumpasis, D.M.13
Tung, C.-S.14
Von Kitzing, E.15
-
14
-
-
0019558179
-
Structure of a B-DNA dodecamer: Conformation and dynamics
-
Drew H. R., Wing R. M., Takano T., Broka C., Tanaka S., Itakura K., Dickerson R. E. Structure of a B-DNA dodecamer: conformation and dynamics. Proc. Natl Acad. Sci. USA. 78:1981;2179-2183.
-
(1981)
Proc. Natl Acad. Sci. USA
, vol.78
, pp. 2179-2183
-
-
Drew, H.R.1
Wing, R.M.2
Takano, T.3
Broka, C.4
Tanaka, S.5
Itakura, K.6
Dickerson, R.E.7
-
15
-
-
0029126044
-
The assessment of the geometry of dinucleotide steps in double-helical DNA: A new local calculation scheme
-
El Hassan M. A., Calladine C. R. The assessment of the geometry of dinucleotide steps in double-helical DNA: a new local calculation scheme. J. Mol. Biol. 251:1995;648-664.
-
(1995)
J. Mol. Biol.
, vol.251
, pp. 648-664
-
-
El Hassan, M.A.1
Calladine, C.R.2
-
16
-
-
3142518260
-
Conformational characteristics of DNA: Empirical classifications and a hypothesis for the conformational behaviour of dinucleotide steps
-
El Hassan M. A., Calladine C. R. Conformational characteristics of DNA: empirical classifications and a hypothesis for the conformational behaviour of dinucleotide steps. Phil. Trans. Roy. Soc. London. 355:1997;43-100.
-
(1997)
Phil. Trans. Roy. Soc. London
, vol.355
, pp. 43-100
-
-
El Hassan, M.A.1
Calladine, C.R.2
-
17
-
-
0030768850
-
Structural variability of the A-DNA in crystals of d(pCpCpCpGpCpGpGpG)
-
Fernandez L. G., Subirana J. A., Verdaguer N., Pyshnyi D., Campos L., Malinina L. Structural variability of the A-DNA in crystals of d(pCpCpCpGpCpGpGpG). J. Biomol. Struct. Dynam. 15:1997;15l-163.
-
(1997)
J. Biomol. Struct. Dynam.
, vol.15
-
-
Fernandez, L.G.1
Subirana, J.A.2
Verdaguer, N.3
Pyshnyi, D.4
Campos, L.5
Malinina, L.6
-
19
-
-
0020359857
-
Reversible bending and helix geometry in a B-DNA dodecamer - CGCGAATTBrCGCG
-
Fratini A. V., Kopka M. L., Drew H. R., Dickerson R. E. Reversible bending and helix geometry in a B-DNA dodecamer - CGCGAATTBrCGCG. J. Biol. Chem. 257:1982;4686-4470.
-
(1982)
J. Biol. Chem.
, vol.257
, pp. 4686-4470
-
-
Fratini, A.V.1
Kopka, M.L.2
Drew, H.R.3
Dickerson, R.E.4
-
20
-
-
0028931709
-
B-DNA twisting correlates with base-pair morphology
-
Gorin A. A., Zhurkin V. B., Olson W. K. B-DNA twisting correlates with base-pair morphology. J. Mol. Biol. 247:1995;34-48.
-
(1995)
J. Mol. Biol.
, vol.247
, pp. 34-48
-
-
Gorin, A.A.1
Zhurkin, V.B.2
Olson, W.K.3
-
21
-
-
0030040722
-
A novel form of the DNA double helix imposed on the TATA-box by the TATA-binding protein
-
Guzikevich-Guerstein G., Shakked Z. A novel form of the DNA double helix imposed on the TATA-box by the TATA-binding protein. Nature Struct. Biol. 3:1996;32-37.
-
(1996)
Nature Struct. Biol.
, vol.3
, pp. 32-37
-
-
Guzikevich-Guerstein, G.1
Shakked, Z.2
-
22
-
-
0031556948
-
DNA base-stacking interactions: A comparison of theoretical calculations with oligonucleotide X-ray crystal structures
-
Hunter C. A., Lu X. J. DNA base-stacking interactions: a comparison of theoretical calculations with oligonucleotide X-ray crystal structures. J. Mol. Biol. 265:1997;603-619.
-
(1997)
J. Mol. Biol.
, vol.265
, pp. 603-619
-
-
Hunter, C.A.1
Lu, X.J.2
-
23
-
-
0030590260
-
How proteins recognize the TATA box
-
Juo Z. S., Chiu T. K., Leiberman P. M., Baikalov I., Berk A. J., Dickerson R. E. How proteins recognize the TATA box. J. Mol. Biol. 261:1996;239-254.
-
(1996)
J. Mol. Biol.
, vol.261
, pp. 239-254
-
-
Juo, Z.S.1
Chiu, T.K.2
Leiberman, P.M.3
Baikalov, I.4
Berk, A.J.5
Dickerson, R.E.6
-
24
-
-
0025187081
-
Refinement of Eco RI endonuclease crystal structure: A revised protein chain tracing
-
Kim Y., Grable J. C., Love R., Greene P. J., Rosenberg J. M. Refinement of Eco RI endonuclease crystal structure: a revised protein chain tracing. Science. 249:1990;1307-1309.
-
(1990)
Science
, vol.249
, pp. 1307-1309
-
-
Kim, Y.1
Grable, J.C.2
Love, R.3
Greene, P.J.4
Rosenberg, J.M.5
-
25
-
-
0027504913
-
Crystal structure of a yeast TBP/TATA-box complex
-
Kim Y., Geiger J. H., Halm S., Sigler P. B. Crystal structure of a yeast TBP/TATA-box complex. Nature. 365:1993;512-520.
-
(1993)
Nature
, vol.365
, pp. 512-520
-
-
Kim, Y.1
Geiger, J.H.2
Halm, S.3
Sigler, P.B.4
-
26
-
-
0028010888
-
HhaI methyltransferase flips its target base out of the DNA helix
-
Klimasauskas S., Kumar S., Roberts R. J., Cheng X. HhaI methyltransferase flips its target base out of the DNA helix. Cell. 76:1994;357-369.
-
(1994)
Cell
, vol.76
, pp. 357-369
-
-
Klimasauskas, S.1
Kumar, S.2
Roberts, R.J.3
Cheng, X.4
-
27
-
-
0024058085
-
The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids
-
Lavery R., Sklenar H. The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids. J. Biomol. Struct. Dynam. 6:1988;63-91.
-
(1988)
J. Biomol. Struct. Dynam.
, vol.6
, pp. 63-91
-
-
Lavery, R.1
Sklenar, H.2
-
28
-
-
0024539180
-
Defining the structure of irregular nucleic acids: Conventions and principles
-
Lavery R., Sklenar H. Defining the structure of irregular nucleic acids: conventions and principles. J. Biomol. Struct. Dynam. 6:1989;655-667.
-
(1989)
J. Biomol. Struct. Dynam.
, vol.6
, pp. 655-667
-
-
Lavery, R.1
Sklenar, H.2
-
29
-
-
0018866122
-
Left-handed DNA helices
-
Leslie A. G. W., Arnott S., Chandrasekaran R., Birdsall D. L., Ratlif R. L. Left-handed DNA helices. Nature. 283:1980;743-746.
-
(1980)
Nature
, vol.283
, pp. 743-746
-
-
Leslie, A.G.W.1
Arnott, S.2
Chandrasekaran, R.3
Birdsall, D.L.4
Ratlif, R.L.5
-
30
-
-
0021095856
-
Protein folding by restrained energy minimization and molecular dynamics
-
Levitt M. Protein folding by restrained energy minimization and molecular dynamics. J. Mol. Biol. 170:1983;723-764.
-
(1983)
J. Mol. Biol.
, vol.170
, pp. 723-764
-
-
Levitt, M.1
-
31
-
-
0031592942
-
Structure and conformation of helical nucleic acids: Analysis program (SCHNAaP)
-
Lu X. J., El Hassan M. A., Hunter C. A. Structure and conformation of helical nucleic acids: analysis program (SCHNAaP). J. Mol. Biol. 273:1997a;668-680.
-
(1997)
J. Mol. Biol.
, vol.273
, pp. 668-680
-
-
Lu, X.J.1
El Hassan, M.A.2
Hunter, C.A.3
-
32
-
-
0031592938
-
Structure and conformation of helical nucleic acids: Rebuilding program (SCHNArP)
-
Lu X. J., El Hassan M. A., Hunter C. A. Structure and conformation of helical nucleic acids: rebuilding program (SCHNArP). J. Mol. Biol. 273:1997b;681-691.
-
(1997)
J. Mol. Biol.
, vol.273
, pp. 681-691
-
-
Lu, X.J.1
El Hassan, M.A.2
Hunter, C.A.3
-
34
-
-
0028923794
-
Comparison of rotation models for describing DNA conformations: Application to static and polymorphic forms
-
Mazur J., Jernigan R. L. Comparison of rotation models for describing DNA conformations: Application to static and polymorphic forms. Biophys. J. 68:1995;1472-1489.
-
(1995)
Biophys. J.
, vol.68
, pp. 1472-1489
-
-
Mazur, J.1
Jernigan, R.L.2
-
35
-
-
0022419269
-
The crystal structure of d(G-G-G-G-C-C-C-C): A model for poly(dG)·poly(dC)
-
McCall M., Brown T., Kermard O. The crystal structure of d(G-G-G-G-C-C-C-C): a model for poly(dG)·poly(dC). J. Mol. Biol. 183:1985;385-396.
-
(1985)
J. Mol. Biol.
, vol.183
, pp. 385-396
-
-
McCall, M.1
Brown, T.2
Kermard, O.3
-
36
-
-
0023513912
-
The structure of an oligo(dA)·oligo(dT) tract and its biological implications
-
Nelson H. C. M., Finch J. T., Luisi B. E., Klug A. The structure of an oligo(dA)·oligo(dT) tract and its biological implications. Nature. 330:1987;221-226.
-
(1987)
Nature
, vol.330
, pp. 221-226
-
-
Nelson, H.C.M.1
Finch, J.T.2
Luisi, B.E.3
Klug, A.4
-
37
-
-
0030005131
-
Simulating DNA at low resolution
-
Olson W. K. Simulating DNA at low resolution. Curr. Opin. Struct. Biol. 6:1996;242-256.
-
(1996)
Curr. Opin. Struct. Biol.
, vol.6
, pp. 242-256
-
-
Olson, W.K.1
-
38
-
-
0027317556
-
Influence of fluctuations on DNA curvature. A comparison of flexible and static wedge models of intrinsically bent DNA
-
Olson W. K., Marky N. L., Jernigan R. L., Zhurkin V. B. Influence of fluctuations on DNA curvature. A comparison of flexible and static wedge models of intrinsically bent DNA. J. Mol. Biol. 232:1993;530-554.
-
(1993)
J. Mol. Biol.
, vol.232
, pp. 530-554
-
-
Olson, W.K.1
Marky, N.L.2
Jernigan, R.L.3
Zhurkin, V.B.4
-
39
-
-
0032530555
-
DNA sequence-dependent deformability deduced from protein-DNA crystal complexes
-
Olson W. K., Gorin A. A., Lu X. J., Hock L. M., Zhurkin V. B. DNA sequence-dependent deformability deduced from protein-DNA crystal complexes. Proc. Natl Acad. Sci. USA. 95:1998;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
-
40
-
-
0031968248
-
Progressive DNA bending is made possible by gradual changes in the torsion angle of the glycosyl bond
-
Pardo L., Pastor N., Weinstein H. Progressive DNA bending is made possible by gradual changes in the torsion angle of the glycosyl bond. Biophys. J. 74:1998;2191-2198.
-
(1998)
Biophys. J.
, vol.74
, pp. 2191-2198
-
-
Pardo, L.1
Pastor, N.2
Weinstein, H.3
-
41
-
-
0027718102
-
Nucleic acids structure analysis: A users guide to a collection of new analysis programs
-
Pednault E. P. D., Babcock M. S., Olson W. K. Nucleic acids structure analysis: a users guide to a collection of new analysis programs. J. Biomol. Struct. Dynam. 11:1993;597-628.
-
(1993)
J. Biomol. Struct. Dynam.
, vol.11
, pp. 597-628
-
-
Pednault, E.P.D.1
Babcock, M.S.2
Olson, W.K.3
-
42
-
-
0030451819
-
Crystal structure of an IHF-DNA complex: A protein-induced DNA U-turn
-
Rice P. A., Yang S. W., Mizuuchi K., Nash H. A. Crystal structure of an IHF-DNA complex: a protein-induced DNA U-turn. Cell. 87:1996;1295-1306.
-
(1996)
Cell
, vol.87
, pp. 1295-1306
-
-
Rice, P.A.1
Yang, S.W.2
Mizuuchi, K.3
Nash, H.A.4
-
44
-
-
84946632750
-
A rigorous basepair oriented description of DNA structures
-
Soumpasis D. M., Tung C. S. A rigorous basepair oriented description of DNA structures. J. Biomol. Struct. Dynam. 6:1988;397-420.
-
(1988)
J. Biomol. Struct. Dynam.
, vol.6
, pp. 397-420
-
-
Soumpasis, D.M.1
Tung, C.S.2
-
45
-
-
84947409428
-
Relationships among rise, cup, roll and stagger in DNA suggested by empirical potential studies of base stacking
-
Sponer J., Kypr J. Relationships among rise, cup, roll and stagger in DNA suggested by empirical potential studies of base stacking. J. Biomol. Struct. Dynam. 11:1993a;27-41.
-
(1993)
J. Biomol. Struct. Dynam.
, vol.11
, pp. 27-41
-
-
Sponer, J.1
Kypr, J.2
-
46
-
-
0027370181
-
Theoretical analysis of the base stacking in DNA: Choice of the force field and a comparison with the oligonucleotide crystal structures
-
Sponer J., Kypr J. Theoretical analysis of the base stacking in DNA: choice of the force field and a comparison with the oligonucleotide crystal structures. J. Biomol. Struct. Dynam. 11:1993b;277-292.
-
(1993)
J. Biomol. Struct. Dynam.
, vol.11
, pp. 277-292
-
-
Sponer, J.1
Kypr, J.2
-
47
-
-
0016670764
-
X-ray crystallographic visualization of drug-nucleic acid intercalative binding: Structure of an ethidium- dinucleoside monophosphate crystalline complex ethidium: 5-iodouridylyl (3′-5′) adenosine
-
Tsai C. C., Jain S. C., Sobell H. M. X-ray crystallographic visualization of drug-nucleic acid intercalative binding: Structure of an ethidium- dinucleoside monophosphate crystalline complex ethidium: 5-iodouridylyl (3′-5′) adenosine. Proc. Natl Acad. Sci. USA. 72:1975;628-632.
-
(1975)
Proc. Natl Acad. Sci. USA
, vol.72
, pp. 628-632
-
-
Tsai, C.C.1
Jain, S.C.2
Sobell, H.M.3
-
48
-
-
0028098726
-
An extension of the rigorous base-unit oriented description of nucleic-acid structures
-
Tung C. S., Soumpasis D. M., Hummer G. An extension of the rigorous base-unit oriented description of nucleic-acid structures. J. Biomol. Struct. Dynam. 11:1994;1327-1344.
-
(1994)
J. Biomol. Struct. Dynam.
, vol.11
, pp. 1327-1344
-
-
Tung, C.S.1
Soumpasis, D.M.2
Hummer, G.3
-
49
-
-
0030046809
-
Intercalation, DNA kinking, and the control of transcription
-
Werner M. E., Gronenborn A. M., Clore G. M. Intercalation, DNA kinking, and the control of transcription. Science. 271:1996;778-784.
-
(1996)
Science
, vol.271
, pp. 778-784
-
-
Werner, M.E.1
Gronenborn, A.M.2
Clore, G.M.3
-
50
-
-
0025966606
-
Analysis of local helix geometry in three B -DNA decamers and eight dodecamers
-
Yanagi K., Privé G. G., Dickerson R. E. Analysis of local helix geometry in three B -DNA decamers and eight dodecamers. J. Mol. Biol. 217:1991;201-214.
-
(1991)
J. Mol. Biol.
, vol.217
, pp. 201-214
-
-
Yanagi, K.1
Privé, G.G.2
Dickerson, R.E.3
-
51
-
-
0018447932
-
Anisotropic flexibility of DNA and the nucleosomal structure
-
Zhurkin V. B., Lysov Y. P., Ivanov V. I. Anisotropic flexibility of DNA and the nucleosomal structure. Nucl. Acids Res. 6:1979;1081-1096.
-
(1979)
Nucl. Acids Res.
, vol.6
, pp. 1081-1096
-
-
Zhurkin, V.B.1
Lysov, Y.P.2
Ivanov, V.I.3
|