-
1
-
-
0032530555
-
DNA sequence-dependent deformability deduced from protein-DNA crystal complexes
-
Olson WK, Gorin AA, Lu X-J, Hock LM, Zhurkin VB. DNA sequence-dependent deformability deduced from protein-DNA crystal complexes. Proc Natl Acad Sci USA 1998, 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
-
2
-
-
40449135396
-
Determining promoter location based on DNA structure first-principles calculations
-
Goni JR, Perez A, Torrents D, Orozco M. Determining promoter location based on DNA structure first-principles calculations. Genome Biol 2007, 8:R263.
-
(2007)
Genome Biol
, vol.8
-
-
Goni, J.R.1
Perez, A.2
Torrents, D.3
Orozco, M.4
-
3
-
-
79958051799
-
DNA shape, genetic codes, and evolution
-
Parker SCJ, Tullius TD. DNA shape, genetic codes, and evolution. Curr Opin Struct Biol 2011, 21:342-347.
-
(2011)
Curr Opin Struct Biol
, vol.21
, pp. 342-347
-
-
Parker, S.C.J.1
Tullius, T.D.2
-
4
-
-
0023187152
-
Effect of non-contacted bases on the affinity of 434 operator for 434 repressor and Cro
-
Koudelka G, Harrison S, Ptashne M. Effect of non-contacted bases on the affinity of 434 operator for 434 repressor and Cro. Nature 1987, 326:886-888.
-
(1987)
Nature
, vol.326
, pp. 886-888
-
-
Koudelka, G.1
Harrison, S.2
Ptashne, M.3
-
5
-
-
0032518220
-
Recognition of DNA structure by 434 repressor
-
Koudelka G. Recognition of DNA structure by 434 repressor. Nucleic Acids Res 1998, 26:669-675.
-
(1998)
Nucleic Acids Res
, vol.26
, pp. 669-675
-
-
Koudelka, G.1
-
6
-
-
39149101474
-
Indirect readout in drug-DNA recognition: role of sequence-dependent DNA conformation
-
Arauzo-Bravo MJ, Sarai A. Indirect readout in drug-DNA recognition: role of sequence-dependent DNA conformation. Nucleic Acids Res 2008, 36:376-386.
-
(2008)
Nucleic Acids Res
, vol.36
, pp. 376-386
-
-
Arauzo-Bravo, M.J.1
Sarai, A.2
-
7
-
-
18744391399
-
Structural dynamics of the lac repressor-DNA complex revealed by a multiscale simulation
-
Villa E, Balaeff A, Schulten K. Structural dynamics of the lac repressor-DNA complex revealed by a multiscale simulation. Proc Natl Acad Sci USA 2005, 102:6783-6788.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 6783-6788
-
-
Villa, E.1
Balaeff, A.2
Schulten, K.3
-
8
-
-
33745595880
-
Modeling the Lac repressor-operator assembly: The influence of DNA looping on Lac repressor conformation
-
Swigon D, Coleman BD, Olson WK. Modeling the Lac repressor-operator assembly: The influence of DNA looping on Lac repressor conformation. Proc Natl Acad Sci USA 2006, 103:9879-9884.
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, pp. 9879-9884
-
-
Swigon, D.1
Coleman, B.D.2
Olson, W.K.3
-
9
-
-
7444244495
-
Core promoter elements of eukaryotic genes have a highly distinctive mechanical property
-
Fukue Y, Sumida N, Nishikawa J, Ohyama T. Core promoter elements of eukaryotic genes have a highly distinctive mechanical property. Nucleic Acids Res 2004, 32:5834-5840.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 5834-5840
-
-
Fukue, Y.1
Sumida, N.2
Nishikawa, J.3
Ohyama, T.4
-
10
-
-
0037992395
-
The structure of DNA in the nucleosome core
-
Richmond TJ, Davey CA. The structure of DNA in the nucleosome core. Nature 2003, 423:145-150.
-
(2003)
Nature
, vol.423
, pp. 145-150
-
-
Richmond, T.J.1
Davey, C.A.2
-
11
-
-
34447644439
-
A novel roll-and-slide mechanism of DNA folding in chromatin: implications for nucleosome positioning
-
Tolstorukov MY, Colasanti AV, McCandlish DM, Olson WK, Zhurkin VB. A novel roll-and-slide mechanism of DNA folding in chromatin: implications for nucleosome positioning. J Mol Biol 2007, 371:725-738.
-
(2007)
J Mol Biol
, vol.371
, pp. 725-738
-
-
Tolstorukov, M.Y.1
Colasanti, A.V.2
McCandlish, D.M.3
Olson, W.K.4
Zhurkin, V.B.5
-
12
-
-
66149110385
-
DNA sequence-directed organization of chromatin: Structure-based computational analysis of nucleosome-binding sequences
-
Balasubramanian S, Xu F, Olson WK. DNA sequence-directed organization of chromatin: Structure-based computational analysis of nucleosome-binding sequences. Biophys J 2009, 96:2245-2260.
-
(2009)
Biophys J
, vol.96
, pp. 2245-2260
-
-
Balasubramanian, S.1
Xu, F.2
Olson, W.K.3
-
13
-
-
60349115060
-
Poly(dA:dT) tracts: major determinants of nucleosome organization
-
Segal E, Widom J. Poly(dA:dT) tracts: major determinants of nucleosome organization. Curr Opin Struct Biol 2009, 19:65-71.
-
(2009)
Curr Opin Struct Biol
, vol.19
, pp. 65-71
-
-
Segal, E.1
Widom, J.2
-
14
-
-
77954659099
-
Relationship between nucleosome positioning and DNA methylation
-
Chodavarapu RK, Feng S, Bernatavichute YV, Chen P-Y, Stroud H, Yu Y, Hetzel JA, Kuo F, Kim J, Cokus SJ, et al. Relationship between nucleosome positioning and DNA methylation. Nature 2010, 466:388-392.
-
(2010)
Nature
, vol.466
, pp. 388-392
-
-
Chodavarapu, R.K.1
Feng, S.2
Bernatavichute, Y.V.3
Chen, P.-Y.4
Stroud, H.5
Yu, Y.6
Hetzel, J.A.7
Kuo, F.8
Kim, J.9
Cokus, S.J.10
-
15
-
-
84860437700
-
Impact of methylation on the physical properties of DNA
-
Perez A, Castellazzi CL, Battistini F, Collinet K, Flores O, Deniz O, Ruiz ML, Torrents D, Eritja R, Soler-Lopez M, et al. Impact of methylation on the physical properties of DNA. Biophys J 2012, 102:2140-2148.
-
(2012)
Biophys J
, vol.102
, pp. 2140-2148
-
-
Perez, A.1
Castellazzi, C.L.2
Battistini, F.3
Collinet, K.4
Flores, O.5
Deniz, O.6
Ruiz, M.L.7
Torrents, D.8
Eritja, R.9
Soler-Lopez, M.10
-
16
-
-
84867508975
-
Sequence-dependent thermodynamics of a coarse-grained DNA model
-
Sulc P, Romano F, Ouldridge TE, Rovigatti L, Doye JPK, Louis AA. Sequence-dependent thermodynamics of a coarse-grained DNA model. J Chem Phys 2012, 137:135101.
-
(2012)
J Chem Phys
, vol.137
, pp. 135101
-
-
Sulc, P.1
Romano, F.2
Ouldridge, T.E.3
Rovigatti, L.4
Doye, J.P.K.5
Louis, A.A.6
-
17
-
-
84864599207
-
Breathing, bubbling, and bending: DNA flexibility from multimicrosecond simulations
-
Zeida A, Machado MR, Dans PD, Pantano S. Breathing, bubbling, and bending: DNA flexibility from multimicrosecond simulations. Phys Rev E 2012, 86:021903.
-
(2012)
Phys Rev E
, vol.86
, pp. 021903
-
-
Zeida, A.1
Machado, M.R.2
Dans, P.D.3
Pantano, S.4
-
18
-
-
0000323998
-
A continuum rod model of sequence-dependent DNA structure
-
Manning RS, Maddocks JH, Kahn JD. A continuum rod model of sequence-dependent DNA structure. J Chem Phys 1996, 105:5626-5646.
-
(1996)
J Chem Phys
, vol.105
, pp. 5626-5646
-
-
Manning, R.S.1
Maddocks, J.H.2
Kahn, J.D.3
-
19
-
-
17944383822
-
Elastic rod model of a DNA loop in the Lac operon
-
Balaeff A, Mahadevan L, Schulten K. Elastic rod model of a DNA loop in the Lac operon. Phys Rev Lett 1999, 83:4900-4903.
-
(1999)
Phys Rev Lett
, vol.83
, pp. 4900-4903
-
-
Balaeff, A.1
Mahadevan, L.2
Schulten, K.3
-
20
-
-
0038298831
-
Theory of sequence-dependent DNA elasticity
-
Coleman BD, Olson WK, Swigon D. Theory of sequence-dependent DNA elasticity. J Chem Phys 2003, 118:7127-7140.
-
(2003)
J Chem Phys
, vol.118
, pp. 7127-7140
-
-
Coleman, B.D.1
Olson, W.K.2
Swigon, D.3
-
21
-
-
84872584744
-
Modelling nucleic acid structure and flexibility: from atomic to mesoscopic scale
-
Schlick T, ed. London: Royal Society of Chemistry
-
Lankas F. Modelling nucleic acid structure and flexibility: from atomic to mesoscopic scale. In: Schlick T, ed. Innovations in Biomolecular Modeling and Simulations. Vol. 2. London: Royal Society of Chemistry; 2012, 3-32.
-
(2012)
Innovations in Biomolecular Modeling and Simulations
, vol.2
, pp. 3-32
-
-
Lankas, F.1
-
22
-
-
0035850731
-
A standard reference frame for the description of nucleic acid base-pair geometry
-
Olson WK, Bansal M, Burley SK, Dickerson RE, Gerstein M, Harvey SC, Heinemann U, Lu X-J, Neidle S, Shakked Z, et al. A standard reference frame for the description of nucleic acid base-pair geometry. J Mol Biol 2001, 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
-
23
-
-
0024974308
-
Definitions and nomenclature of nucleic acid structure parameters
-
Dickerson RE, Bansal M, Calladine CR, Diekmann S, Hunter WN, Kennard O, Lavery R, Nelson HCM, Olson WK, Saenger W, et al. Definitions and nomenclature of nucleic acid structure parameters. J Mol Biol 1989, 205:787-791.
-
(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.K.9
Saenger, W.10
-
24
-
-
0242396923
-
3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures
-
Lu X-J, Olson WK. 3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. Nucleic Acids Res 2003, 31:5108-5121.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 5108-5121
-
-
Lu, X.-J.1
Olson, W.K.2
-
25
-
-
70450261721
-
Conformational analysis of nucleic acids revisited: Curves+
-
Lavery R, Moakher M, Maddocks JH, Petkeviciute D, Zakrzewska K. Conformational analysis of nucleic acids revisited: Curves+. Nucleic Acids Res 2009, 37:5917-5929.
-
(2009)
Nucleic Acids Res
, vol.37
, pp. 5917-5929
-
-
Lavery, R.1
Moakher, M.2
Maddocks, J.H.3
Petkeviciute, D.4
Zakrzewska, K.5
-
26
-
-
0035595722
-
Extracting parameters for base-pair level models of DNA from molecular dynamics simulations
-
Gonzalez O, Maddocks JH. Extracting parameters for base-pair level models of DNA from molecular dynamics simulations. Theor Chem Acc 2001, 106:76-82.
-
(2001)
Theor Chem Acc
, vol.106
, pp. 76-82
-
-
Gonzalez, O.1
Maddocks, J.H.2
-
27
-
-
70450267492
-
On the parameterization of rigid base and basepair models of DNA from molecular dynamics simulations
-
Lankas F, Gonzalez O, Heffler LM, Stoll G, Moakher M, Maddocks JH. On the parameterization of rigid base and basepair models of DNA from molecular dynamics simulations. Phys Chem Chem Phys 2009, 11:10565-10588.
-
(2009)
Phys Chem Chem Phys
, vol.11
, pp. 10565-10588
-
-
Lankas, F.1
Gonzalez, O.2
Heffler, L.M.3
Stoll, G.4
Moakher, M.5
Maddocks, J.H.6
-
28
-
-
0242290881
-
DNA basepair step deformability inferred from molecular dynamics simulations
-
Lankas F, Sponer J, Langowski J, Cheatham TE III DNA basepair step deformability inferred from molecular dynamics simulations. Biophys J 2003, 85:2872-2883.
-
(2003)
Biophys J
, vol.85
, pp. 2872-2883
-
-
Lankas, F.1
Sponer, J.2
Langowski, J.3
Cheatham, T.E.4
-
30
-
-
84872151052
-
Structure, stiffness and substates of the Dickerson-Drew dodecamer
-
Drsata T, Perez A, Orozco M, Morozov AV, Sponer J, Lankas F. Structure, stiffness and substates of the Dickerson-Drew dodecamer. J Chem Theory Comput 2013, 9:707-721.
-
(2013)
J Chem Theory Comput
, vol.9
, pp. 707-721
-
-
Drsata, T.1
Perez, A.2
Orozco, M.3
Morozov, A.V.4
Sponer, J.5
Lankas, F.6
-
31
-
-
35548987996
-
Sequence-dependent DNA deformability studied using molecular dynamics simulations
-
Fujii S, Kono H, Takenaka S, Go N, Sarai A. Sequence-dependent DNA deformability studied using molecular dynamics simulations. Nucleic Acids Res 2007, 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
-
32
-
-
33751003527
-
Indirect readout: detection of optimized subsequences and calculation of relative binding affinities using different DNA elastic potentials
-
Becker NB, Wolff L, Everaers R. Indirect readout: detection of optimized subsequences and calculation of relative binding affinities using different DNA elastic potentials. Nucleic Acids Res 2006, 34:5638-5649.
-
(2006)
Nucleic Acids Res
, vol.34
, pp. 5638-5649
-
-
Becker, N.B.1
Wolff, L.2
Everaers, R.3
-
33
-
-
34548187754
-
From rigid base pairs to semiflexible polymers: coarse-graining DNA
-
Becker N, Everaers R. From rigid base pairs to semiflexible polymers: coarse-graining DNA. Phys Rev E 2007, 76:021923.
-
(2007)
Phys Rev E
, vol.76
, pp. 021923
-
-
Becker, N.1
Everaers, R.2
-
34
-
-
64049116057
-
DNA nanomechanics in the nucleosome
-
Becker NB, Everaers R. DNA nanomechanics in the nucleosome. Structure 2009, 17:579-589.
-
(2009)
Structure
, vol.17
, pp. 579-589
-
-
Becker, N.B.1
Everaers, R.2
-
35
-
-
77953104932
-
Single-base resolution mapping of H1-nucleosome interactions and 3D organization of the nucleosome
-
Syed SH, Goutte-Gattat D, Becker NB, Meyer S, Shukla MS, Hayes JJ, Everaers R, Angelov D, Bednar J, Dimitrov S. Single-base resolution mapping of H1-nucleosome interactions and 3D organization of the nucleosome. Proc Natl Acad Sci USA 2010, 107:9620-9625.
-
(2010)
Proc Natl Acad Sci USA
, vol.107
, pp. 9620-9625
-
-
Syed, S.H.1
Goutte-Gattat, D.2
Becker, N.B.3
Meyer, S.4
Shukla, M.S.5
Hayes, J.J.6
Everaers, R.7
Angelov, D.8
Bednar, J.9
Dimitrov, S.10
-
36
-
-
1842607449
-
DNA deformability at the base pair level
-
Lankas F, Sponer J, Langowski J, Cheatham TE III DNA deformability at the base pair level. J Am Chem Soc 2004, 126:4124-4125.
-
(2004)
J Am Chem Soc
, vol.126
, pp. 4124-4125
-
-
Lankas, F.1
Sponer, J.2
Langowski, J.3
Cheatham, T.E.4
-
37
-
-
28044444099
-
Sequence-dependent conformational energy of DNA derived from molecular dynamics simulations: toward understanding the indirect readout mechanism in protein-DNA recognition
-
Arauzo-Bravo MJ, Fujii S, Kono H, Ahmad S, Sarai A. 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 2005, 127:16074-16089.
-
(2005)
J Am Chem Soc
, vol.127
, pp. 16074-16089
-
-
Arauzo-Bravo, M.J.1
Fujii, S.2
Kono, H.3
Ahmad, S.4
Sarai, A.5
-
38
-
-
70450248170
-
A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA
-
Lavery R, Zakrzewska K, Beveridge DL, Bishop TC, Case DA, Cheatham TE Cheatham, Dixit SB, Jayaram B, Lankas F, Laughton C, et al. A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA. Nucleic Acids Res 2010, 38:299-313.
-
(2010)
Nucleic Acids Res
, vol.38
, pp. 299-313
-
-
Lavery, R.1
Zakrzewska, K.2
Beveridge, D.L.3
Bishop, T.C.4
Case, D.A.5
Cheatham, T.E.6
Dixit, S.B.7
Jayaram, B.8
Lankas, F.9
Laughton, C.10
-
39
-
-
77953697462
-
A measure of bending in nucleic acids structures applied to A-tract DNA
-
Lankas F, Spackova N, Moakher M, Enkhbayar P, Sponer J. A measure of bending in nucleic acids structures applied to A-tract DNA. Nucleic Acids Res 2010, 38:3414-3422.
-
(2010)
Nucleic Acids Res
, vol.38
, pp. 3414-3422
-
-
Lankas, F.1
Spackova, N.2
Moakher, M.3
Enkhbayar, P.4
Sponer, J.5
-
40
-
-
84879110345
-
-
AMBER
-
Case DA, Darden TA, Cheatham TE III, Simmerling CL, Wang J, Duke RE, Luo R, Walker RC, Zhang W, Merz KM, et al. AMBER 12; 2012.
-
(2012)
, vol.12
-
-
Case, D.A.1
Darden, T.A.2
Cheatham, T.I.3
Simmerling, C.L.4
Wang, J.5
Duke, R.E.6
Luo, R.7
Walker, R.C.8
Zhang, W.9
Merz, K.M.10
-
41
-
-
34250318638
-
Refinenement of the AMBER force field for nucleic acids: Improving the description of alpha/gamma conformers
-
Perez A, Marchan I, Svozil D, Sponer J, Cheatham TE, Laughton CA, Orozco M. Refinenement of the AMBER force field for nucleic acids: Improving the description of alpha/gamma conformers. Biophys J 2007, 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.5
Laughton, C.A.6
Orozco, M.7
-
42
-
-
1242314385
-
DNA fine structure and dynamics in crystals and in solution: the impact of BI/BII backbone conformations
-
Djuranovic D, Hartmann B. DNA fine structure and dynamics in crystals and in solution: the impact of BI/BII backbone conformations. Biopolymers 2004, 73:356-368.
-
(2004)
Biopolymers
, vol.73
, pp. 356-368
-
-
Djuranovic, D.1
Hartmann, B.2
-
43
-
-
84860376513
-
B-DNA structure is intrinsically polymorphic: even at the level of base pair positions
-
Maehigashi T, Hsiao C, Woods KK, Moulaei T, Hud NV, Williams LD. B-DNA structure is intrinsically polymorphic: even at the level of base pair positions. Nucleic Acids Res 2012, 40:3714-3722.
-
(2012)
Nucleic Acids Res
, vol.40
, pp. 3714-3722
-
-
Maehigashi, T.1
Hsiao, C.2
Woods, K.K.3
Moulaei, T.4
Hud, N.V.5
Williams, L.D.6
-
44
-
-
76149104568
-
A generalized conformational energy function of DNA derived from molecular dynamics simulations
-
Yamasaki S, Terada T, Shimizu K, Kono H, Sarai A. A generalized conformational energy function of DNA derived from molecular dynamics simulations. Nucleic Acids Res 2009, 37:e135.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Yamasaki, S.1
Terada, T.2
Shimizu, K.3
Kono, H.4
Sarai, A.5
-
45
-
-
84870578921
-
Exploring polymorphisms in B-DNA helical conformations
-
Dans PD, Perez A, Faustino I, Lavery R, Orozco M. Exploring polymorphisms in B-DNA helical conformations. Nucleic Acids Res 2012, 40:10668-10678.
-
(2012)
Nucleic Acids Res
, vol.40
, pp. 10668-10678
-
-
Dans, P.D.1
Perez, A.2
Faustino, I.3
Lavery, R.4
Orozco, M.5
|