-
1
-
-
0038497542
-
Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid
-
Watson, J.D. and Crick, F.H. (1953) Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid. Nature, 171, 737-738.
-
(1953)
Nature
, vol.171
, pp. 737-738
-
-
Watson, J.D.1
Crick, F.H.2
-
3
-
-
0015525307
-
Optimised parameters for RNA double-helices
-
Arnott, S., Hukins, D.W. and Dover, S.D. (1972) Optimised parameters for RNA double-helices. Biochem. Biophys. Res. Commun., 48, 1392-1399.
-
(1972)
Biochem. Biophys. Res. Commun.
, vol.48
, pp. 1392-1399
-
-
Arnott, S.1
Hukins, D.W.2
Dover, S.D.3
-
4
-
-
0016299918
-
Structural details of double-helix observed for DNAs containing alternating purine and pyrimidine sequences
-
Arnott, S., Chandrasekaran, R., Hukins, D.W., Smith, P.J. and Watts, L. (1974) Structural details of double-helix observed for DNAs containing alternating purine and pyrimidine sequences. J. Mol. Biol., 88, 523-533.
-
(1974)
J. Mol. Biol.
, vol.88
, pp. 523-533
-
-
Arnott, S.1
Chandrasekaran, R.2
Hukins, D.W.3
Smith, P.J.4
Watts, L.5
-
5
-
-
0019326076
-
Polymorphism of DNA double helices
-
Leslie, A.G., Arnott, S., Chandrasekaran, R. and Ratliff, R.L. (1980) Polymorphism of DNA double helices. J. Mol. Biol., 143, 49-72.
-
(1980)
J. Mol. Biol.
, vol.143
, pp. 49-72
-
-
Leslie, A.G.1
Arnott, S.2
Chandrasekaran, R.3
Ratliff, R.L.4
-
7
-
-
0017098687
-
RNA double helices generated from crystal structures of double helical dinucleoside phosphates
-
Rosenberg, J.M., Seeman, N.C., Day, R.O. and Rich, A. (1976) RNA double helices generated from crystal structures of double helical dinucleoside phosphates. Biochem. Biophys. Res. Commun., 69, 979-987.
-
(1976)
Biochem. Biophys. Res. Commun.
, vol.69
, pp. 979-987
-
-
Rosenberg, J.M.1
Seeman, N.C.2
Day, R.O.3
Rich, A.4
-
8
-
-
0019387686
-
Structure of a B-DNA dodecamer. II. Influence of base sequence on helix structure
-
Dickerson, R.E. and Drew, H.R. (1981) Structure of a B-DNA dodecamer. II. Influence of base sequence on helix structure. J. Mol. Biol., 149, 761-786.
-
(1981)
J. Mol. Biol.
, vol.149
, pp. 761-786
-
-
Dickerson, R.E.1
Drew, H.R.2
-
9
-
-
0020359857
-
Reversible bending and helix geometry in a B-DNA dodecamer: CGCGAATTBrCGCG
-
Fratini, A.V., Kopka, M.L., Drew, H.R. and Dickerson, R.E. (1982) Reversible bending and helix geometry in a B-DNA dodecamer: CGCGAATTBrCGCG. J. Biol. Chem., 257, 14686-14707.
-
(1982)
J. Biol. Chem.
, vol.257
, pp. 14686-14707
-
-
Fratini, A.V.1
Kopka, M.L.2
Drew, H.R.3
Dickerson, R.E.4
-
10
-
-
0024599312
-
Definitions and nomenclature of nucleic acid structure components
-
Dickerson, R.E. (1989) Definitions and nomenclature of nucleic acid structure components. Nucleic Acids Res., 17, 1797-1803.
-
(1989)
Nucleic Acids Res.
, vol.17
, pp. 1797-1803
-
-
Dickerson, R.E.1
-
11
-
-
0032950260
-
Overview of nucleic acid analysis programs
-
Lu, X.J., Babcock, M.S. and Olson, W.K. (1999) Overview of nucleic acid analysis programs. J. Biomol. Struct. Dyn., 16, 833-843.
-
(1999)
J. Biomol. Struct. Dyn.
, vol.16
, pp. 833-843
-
-
Lu, X.J.1
Babcock, M.S.2
Olson, W.K.3
-
12
-
-
0028221654
-
The effect of mathematics and coordinate system on comparability and 'dependencies' of nucleic acid structure parameters
-
Babcock, M.S. and Olson, W.K. (1994) The effect of mathematics and coordinate system on comparability and 'dependencies' of nucleic acid structure parameters. J. Mol. Biol., 237, 98-124.
-
(1994)
J. Mol. Biol.
, vol.237
, pp. 98-124
-
-
Babcock, M.S.1
Olson, W.K.2
-
13
-
-
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. 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
-
14
-
-
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
-
15
-
-
50349085962
-
3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures
-
Lu, X.J. and Olson, W.K. (2008) 3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures. Nat. Protocols, 3, 1213-1227.
-
(2008)
Nat. Protocols
, vol.3
, pp. 1213-1227
-
-
Lu, X.J.1
Olson, W.K.2
-
16
-
-
0024539180
-
Defining the structure of irregular nucleic acids: conventions and principles
-
Lavery, R. and Sklenar, H. (1989) Defining the structure of irregular nucleic acids: conventions and principles. J. Biomol. Struct. Dyn., 6, 655-667.
-
(1989)
J. Biomol. Struct. Dyn.
, vol.6
, pp. 655-667
-
-
Lavery, R.1
Sklenar, H.2
-
17
-
-
0024058085
-
The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids
-
Lavery, R. and Sklenar, H. (1988) The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids. J. Biomol. Struct. Dyn., 6, 63-91.
-
(1988)
J. Biomol. Struct. Dyn.
, vol.6
, pp. 63-91
-
-
Lavery, R.1
Sklenar, H.2
-
18
-
-
0037992395
-
The structure of DNA in the nucleosome core
-
Richmond, T.J. and Davey, C.A. (2003) The structure of DNA in the nucleosome core. Nature, 423, 145-150.
-
(2003)
Nature
, vol.423
, pp. 145-150
-
-
Richmond, T.J.1
Davey, C.A.2
-
19
-
-
44349162159
-
Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structures
-
Chen, Z., Yang, H. and Pavletich, N.P. (2008) Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structures. Nature, 453, 489-494.
-
(2008)
Nature
, vol.453
, pp. 489-494
-
-
Chen, Z.1
Yang, H.2
Pavletich, N.P.3
-
20
-
-
0030064676
-
DNA: an extensible molecule
-
Cluzel, P., Lebrun, A., Heller, C., Lavery, R., Viovy, J.L., Chatenay, D. and Caron, F. (1996) DNA: an extensible molecule. Science, 271, 792-794.
-
(1996)
Science
, vol.271
, pp. 792-794
-
-
Cluzel, P.1
Lebrun, A.2
Heller, C.3
Lavery, R.4
Viovy, J.L.5
Chatenay, D.6
Caron, F.7
-
21
-
-
0030024985
-
Overstretching B-DNA: the elastic response of individual double-stranded and single-stranded DNA molecules
-
Smith, S.B., Cui, Y. and Bustamante, C. (1996) Overstretching B-DNA: the elastic response of individual double-stranded and single-stranded DNA molecules. Science, 271, 795-799.
-
(1996)
Science
, vol.271
, pp. 795-799
-
-
Smith, S.B.1
Cui, Y.2
Bustamante, C.3
-
22
-
-
0032564447
-
Stretched and overwound DNA forms a Pauling-like structure with exposed bases
-
Allemand, J.F., Bensimon, D., Lavery, R. and Croquette, V. (1998) Stretched and overwound DNA forms a Pauling-like structure with exposed bases. Proc. Natl Acad. Sci. USA, 95, 14152-14157.
-
(1998)
Proc. Natl Acad. Sci. USA
, vol.95
, pp. 14152-14157
-
-
Allemand, J.F.1
Bensimon, D.2
Lavery, R.3
Croquette, V.4
-
23
-
-
42149084972
-
Recent advances in the study of nucleic acid flexibility by molecular dynamics
-
Orozco, M., Noy, A. and Pérez, A. (2008) Recent advances in the study of nucleic acid flexibility by molecular dynamics. Curr. Opin. Struct. Biol., 18, 185-193.
-
(2008)
Curr. Opin. Struct. Biol.
, vol.18
, pp. 185-193
-
-
Orozco, M.1
Noy, A.2
Pérez, A.3
-
24
-
-
41949124146
-
Molecular dynamics simulations of nucleic acid-protein complexes
-
Mackerell, A.D. and Nilsson, L. (2008) Molecular dynamics simulations of nucleic acid-protein complexes. Curr. Opin. Struct. Biol., 18, 194-199.
-
(2008)
Curr. Opin. Struct. Biol.
, vol.18
, pp. 194-199
-
-
Mackerell, A.D.1
Nilsson, L.2
-
25
-
-
0033614014
-
Resolving the discrepancies among nucleic acid conformational analyses
-
Lu, X.J. and Olson, W.K. (1999) Resolving the discrepancies among nucleic acid conformational analyses. J. Mol. Biol., 285, 1563-1575.
-
(1999)
J. Mol. Biol.
, vol.285
, pp. 1563-1575
-
-
Lu, X.J.1
Olson, W.K.2
-
26
-
-
0018350099
-
Gene duplications in the structural evolution of chymotrypsin
-
McLachlan, A.D. (1979) Gene duplications in the structural evolution of chymotrypsin. J. Mol. Biol., 128, 49-79.
-
(1979)
J. Mol. Biol.
, vol.128
, pp. 49-79
-
-
McLachlan, A.D.1
-
27
-
-
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. and Olson, W.K. (1994) Nucleic acid structure analysis. Mathematics for local Cartesian and helical structure parameters that are truly comparable between structures. J. Mol. Biol., 237, 125-156.
-
(1994)
J. Mol. Biol.
, vol.237
, pp. 125-156
-
-
Babcock, M.S.1
Pednault, E.P.2
Olson, W.K.3
-
28
-
-
0028923794
-
Comparison of rotation models for describing DNA conformations: application to static and polymorphic forms
-
Mazur, J. and Jernigan, R.L. (1995) Comparison of rotation models for describing DNA conformations: application to static and polymorphic forms. Biophys. J., 68, 1472-1489.
-
(1995)
Biophys. J.
, vol.68
, pp. 1472-1489
-
-
Mazur, J.1
Jernigan, R.L.2
-
29
-
-
0035595722
-
Extracting parameters for base-pair level models of DNAfrom molecular dynamics simulations
-
Maddocks, J.H. and Gonzalez, O. (2001) Extracting parameters for base-pair level models of DNAfrom molecular dynamics simulations. Theor. Chem. Acc., 106, 76-82.
-
(2001)
Theor. Chem. Acc.
, vol.106
, pp. 76-82
-
-
Maddocks, J.H.1
Gonzalez, O.2
-
30
-
-
0031398581
-
Estimators for the standard deviation of horizontal wind direction
-
Weber, R.O. (1997) Estimators for the standard deviation of horizontal wind direction. J. Appl. Meteorol., 36, 1403-1415.
-
(1997)
J. Appl. Meteorol.
, vol.36
, pp. 1403-1415
-
-
Weber, R.O.1
-
31
-
-
0021203270
-
A comparison of several "single-pass" estimators of the standard deviation of wind direction
-
Yamartino, R.J. (1984) A comparison of several "single-pass" estimators of the standard deviation of wind direction. J. Climate Appl. Meteorol., 23, 1362-1366.
-
(1984)
J. Climate Appl. Meteorol.
, vol.23
, pp. 1362-1366
-
-
Yamartino, R.J.1
-
32
-
-
0027263885
-
An exact description of five-membered ring configurations. I. Parameterization via an amplitude S, an angle gamma, the pseudorotation amplitude q and phase angle P, and the bond lengths
-
Marzec, C.J. and Day, L.A. (1993) An exact description of five-membered ring configurations. I. Parameterization via an amplitude S, an angle gamma, the pseudorotation amplitude q and phase angle P, and the bond lengths. J. Biomol. Struct. Dyn., 10, 1091-1123.
-
(1993)
J. Biomol. Struct. Dyn.
, vol.10
, pp. 1091-1123
-
-
Marzec, C.J.1
Day, L.A.2
-
33
-
-
0001252431
-
A method for the analysis of puckering disorder in five-membered rings: the relative mobilities of furanose and proline rings and their effects on polynucleotide and polypeptide backbone flexibility
-
Westhof, E. and Sundaralingam, M. (1983) A method for the analysis of puckering disorder in five-membered rings: the relative mobilities of furanose and proline rings and their effects on polynucleotide and polypeptide backbone flexibility. J. Am. Chem. Soc., 105, 970-976.
-
(1983)
J. Am. Chem. Soc.
, vol.105
, pp. 970-976
-
-
Westhof, E.1
Sundaralingam, M.2
-
34
-
-
0027364174
-
PNA hybridizes to complementary oligonucleotides obeying the Watson-Crick hydrogen-bonding rules
-
Egholm, M., Buchardt, O., Christensen, L., Behrens, C., Freier, S.M., Driver, D.A., Berg, R.H., Kim, S.K., Norden, B. and Nielsen, P.E. (1993) PNA hybridizes to complementary oligonucleotides obeying the Watson-Crick hydrogen-bonding rules. Nature, 365, 566-568.
-
(1993)
Nature
, vol.365
, pp. 566-568
-
-
Egholm, M.1
Buchardt, O.2
Christensen, L.3
Behrens, C.4
Freier, S.M.5
Driver, D.A.6
Berg, R.H.7
Kim, S.K.8
Norden, B.9
Nielsen, P.E.10
-
35
-
-
2342518189
-
Spontaneous sharp bending of double-stranded DNA
-
Cloutier, T.E. and Widom, J. (2004) Spontaneous sharp bending of double-stranded DNA. Mol. Cell, 14, 355-362.
-
(2004)
Mol. Cell
, vol.14
, pp. 355-362
-
-
Cloutier, T.E.1
Widom, J.2
-
36
-
-
33749259954
-
Kinking occurs during molecular dynamics simulations of small DNA minicircles
-
Lankas, F., Lavery, R. and Maddocks, J.H. (2006) Kinking occurs during molecular dynamics simulations of small DNA minicircles. Structure, 14, 1527-1534.
-
(2006)
Structure
, vol.14
, pp. 1527-1534
-
-
Lankas, F.1
Lavery, R.2
Maddocks, J.H.3
-
37
-
-
40249090005
-
Kinking the double helix by bending deformation
-
Du, Q., Kotlyar, A. and Vologodskii, A. (2008) Kinking the double helix by bending deformation. Nucleic Acids Res., 36, 1120-1128.
-
(2008)
Nucleic Acids Res.
, vol.36
, pp. 1120-1128
-
-
Du, Q.1
Kotlyar, A.2
Vologodskii, A.3
-
38
-
-
38349173106
-
Mapping the phase diagram of the writhe of DNA nanocircles using atomistic molecular dynamics simulations
-
Harris, S.A., Laughton, C.A. and Liverpool, T.B. (2008) Mapping the phase diagram of the writhe of DNA nanocircles using atomistic molecular dynamics simulations. Nucleic Acids Res., 36, 21-29.
-
(2008)
Nucleic Acids Res.
, vol.36
, pp. 21-29
-
-
Harris, S.A.1
Laughton, C.A.2
Liverpool, T.B.3
-
39
-
-
45249118115
-
Supercoiling and denaturation of DNA loops
-
Liverpool, T.B., Harris, S.A. and Laughton, C.A. (2008) Supercoiling and denaturation of DNA loops. Phys. Rev. Lett., 100, 238103.
-
(2008)
Phys. Rev. Lett.
, vol.100
, pp. 238103
-
-
Liverpool, T.B.1
Harris, S.A.2
Laughton, C.A.3
-
40
-
-
10044257912
-
Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. I. Research design and results on d(CpG) steps
-
Beveridge, D.L., Barreiro, G., Byun, K.S., Case, D.A., Cheatham, T.E.3., Dixit, S.B., Giudice, E., Lankas, F., Lavery, R. et al. (2004) Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. I. Research design and results on d(CpG) steps. Biophys. J., 87, 3799-3813.
-
(2004)
Biophys. J.
, vol.87
, pp. 3799-3813
-
-
Beveridge, D.L.1
Barreiro, G.2
Byun, K.S.3
Case, D.A.4
Cheatham, T.E.3.5
Dixit, S.B.6
Giudice, E.7
Lankas, F.8
Lavery R. et, al.9
-
41
-
-
28444490422
-
Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. II: sequence context effects on the dynamical structures of the 10 unique dinucleotide steps
-
Dixit, S.B., Beveridge, D.L., Case, D.A., Cheatham, T.E. III, Giudice, E., Lankas, F., Lavery, R., Maddocks, J.H., Osman, R. et al. (2005) Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. II: sequence context effects on the dynamical structures of the 10 unique dinucleotide steps. Biophys. J., 89, 3721-3740.
-
(2005)
Biophys. J.
, vol.89
, pp. 3721-3740
-
-
Dixit, S.B.1
Beveridge, D.L.2
Case, D.A.3
Cheatham T.E., III.4
Giudice, E.5
Lankas, F.6
Lavery, R.7
Maddocks, J.H.8
Osman R. et, al.9
-
42
-
-
0019331504
-
Crystal structure analysis of a complete turn of B-DNA
-
Wing, R., Drew, H., Takano, T., Broka, C., Tanaka, S., Itakura, K. and Dickerson, R.E. (1980) Crystal structure analysis of a complete turn of B-DNA. Nature, 287, 755-758.
-
(1980)
Nature
, vol.287
, pp. 755-758
-
-
Wing, R.1
Drew, H.2
Takano, T.3
Broka, C.4
Tanaka, S.5
Itakura, K.6
Dickerson, R.E.7
-
43
-
-
0024672520
-
Molecular structure of an A-DNA decamer d(ACCGGCCGGT)
-
Frederick, C.A., Quigley, G.J., Teng, M.K., Coll, M., Van der Marel, G.A., Van Boom, J.H., Rich, A. and Wang, A.H. (1989) Molecular structure of an A-DNA decamer d(ACCGGCCGGT). Eur. J. Biochem., 181, 295-307.
-
(1989)
Eur. J. Biochem.
, vol.181
, pp. 295-307
-
-
Frederick, C.A.1
Quigley, G.J.2
Teng, M.K.3
Coll, M.4
Van der Marel, G.A.5
Van Boom, J.H.6
Rich, A.7
Wang, A.H.8
-
44
-
-
0029995880
-
Crystal structure of a human TATA box-binding protein/TATA element complex
-
Nikolov, D.B., Chen, H., Halay, E.D., Hoffman, A., Roeder, R.G. and Burley, S.K. (1996) Crystal structure of a human TATA box-binding protein/TATA element complex. Proc. Natl Acad. Sci. USA, 93, 4862-4867.
-
(1996)
Proc. Natl Acad. Sci. USA
, vol.93
, pp. 4862-4867
-
-
Nikolov, D.B.1
Chen, H.2
Halay, E.D.3
Hoffman, A.4
Roeder, R.G.5
Burley, S.K.6
-
45
-
-
0030040722
-
A novel form of the DNA double helix imposed on the TATA-box by the TATA-binding protein
-
Guzikevich-Guerstein, G. and Shakked, Z. (1996) A novel form of the DNA double helix imposed on the TATA-box by the TATA-binding protein. Nat. Struct. Biol., 3, 32-37.
-
(1996)
Nat. Struct. Biol.
, vol.3
, pp. 32-37
-
-
Guzikevich-Guerstein, G.1
Shakked, Z.2
-
46
-
-
0029878720
-
VMD: visual molecular dynamics
-
Humphrey, W., Dalke, A. and Schulten, K. (1996) VMD: visual molecular dynamics. J. Mol. Graph., 14, 33-38.
-
(1996)
J. Mol. Graph.
, vol.14
, pp. 33-38
-
-
Humphrey, W.1
Dalke, A.2
Schulten, K.3
-
47
-
-
0029023343
-
NUPARM and NUCGEN: software for analysis and generation of sequence dependent nucleic acid structures
-
Bansal, M., Bhattacharyya, D. and Ravi, B. (1995) NUPARM and NUCGEN: software for analysis and generation of sequence dependent nucleic acid structures. Comput. Appl. Biosci., 11, 281-287.
-
(1995)
Comput. Appl. Biosci.
, vol.11
, pp. 281-287
-
-
Bansal, M.1
Bhattacharyya, D.2
Ravi, B.3
|