-
2
-
-
0029889473
-
Specificity mechanisms in the control of transcription
-
von Hippel, P. H., W. A. Rees, K. Rippe, and K. S. Wilson. 1996. Specificity mechanisms in the control of transcription. Biophys. Chem. 59:231-246.
-
(1996)
Biophys. Chem.
, vol.59
, pp. 231-246
-
-
Von Hippel, P.H.1
Rees, W.A.2
Rippe, K.3
Wilson, K.S.4
-
3
-
-
0030605506
-
Before an understanding of protein-DNA recognition
-
Rhodes, D., J. W. Schwabe, L. Chapman, and L. Fairall. 1996. Before an understanding of protein-DNA recognition. Philos. Trans. R. Soc. Lond. B Biol. Sci. 351:501-509.
-
(1996)
Philos. Trans. R. Soc. Lond. B Biol. Sci.
, vol.351
, pp. 501-509
-
-
Rhodes, D.1
Schwabe, J.W.2
Chapman, L.3
Fairall, L.4
-
4
-
-
0032530555
-
DNA sequence-dependent deformability deduced from protein-DNA crystal complexes
-
Olson, W. K., A. A. Gorin, X.-J. Lu, L. M. Hock, and V. B. Zhurkin. 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
-
5
-
-
19944428078
-
Chromatin architecture and gene expression in Escherichia coli
-
Willenbrock, H., and D. W. Ussery. 2004. Chromatin architecture and gene expression in Escherichia coli. Genome Biol. 5:252.
-
(2004)
Genome Biol.
, vol.5
, pp. 252
-
-
Willenbrock, H.1
Ussery, D.W.2
-
7
-
-
0022914418
-
The principles of sequence-dependent flexure of DNA
-
Calladine, C. R. 1980. The principles of sequence-dependent flexure of DNA. J. Mol. Biol. 192:907-918.
-
(1980)
J. Mol. Biol.
, vol.192
, pp. 907-918
-
-
Calladine, C.R.1
-
8
-
-
0027318463
-
Sequence-dependent DNA structure. The role of base stacking interactions
-
Hunter, C. A. 1993. Sequence-dependent DNA structure. The role of base stacking interactions. J. Mol. Biol. 230:1025-1054.
-
(1993)
J. Mol. Biol.
, vol.230
, pp. 1025-1054
-
-
Hunter, C.A.1
-
9
-
-
0028931709
-
B-DNA twisting correlates with basepair morphology
-
Gorin, A. A., V. B. Zhurkin, and W. K. Olson. 1995. B-DNA twisting correlates with basepair morphology. J. Mol. Biol. 247:34-48.
-
(1995)
J. Mol. Biol.
, vol.247
, pp. 34-48
-
-
Gorin, A.A.1
Zhurkin, V.B.2
Olson, W.K.3
-
10
-
-
0029126044
-
The assessment of the geometry of dinucleotide steps in double-helical DNA: A new local calculation scheme
-
El Hassan, M. A., and C. R. Calladine. 1995. The assessment of the geometry of dinucleotide steps in double-helical DNA: a new local calculation scheme. J. Mol. Biol. 251:648-664.
-
(1995)
J. Mol. Biol.
, vol.251
, pp. 648-664
-
-
El Hassan, M.A.1
Calladine, C.R.2
-
11
-
-
3142518260
-
Conformational characteristics of DNA: Empirical classifications and a hypothesis for the conformational behaviors of dinucleotide steps
-
El Hassan, M. A., and C. R. Calladine. 1997. Conformational characteristics of DNA: empirical classifications and a hypothesis for the conformational behaviors of dinucleotide steps. Philos. Trans. R. Soc. Lond. A. 355:43-100.
-
(1997)
Philos. Trans. R. Soc. Lond. A
, vol.355
, pp. 43-100
-
-
El Hassan, M.A.1
Calladine, C.R.2
-
12
-
-
0034614487
-
Sequence-dependent DNA structure: Tetranucleotide conformational maps
-
Packer, M. J., M. P. Dauncey, and C. A. Hunter. 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
-
14
-
-
3042572330
-
Implications of the dependence of the elastic properties of DNA on nucleotide sequence
-
Olson, W. K., D. Swigon, and B. D. Coleman. 2004. Implications of the dependence of the elastic properties of DNA on nucleotide sequence. Philos. Trans. R. Soc. Lond. A. 362:1403-1422.
-
(2004)
Philos. Trans. R. Soc. Lond. A
, vol.362
, pp. 1403-1422
-
-
Olson, W.K.1
Swigon, D.2
Coleman, B.D.3
-
15
-
-
3042581815
-
The structural basis of DNA flexibility
-
Travers, A. A. 2004. The structural basis of DNA flexibility. Philos. Trans. R. Soc. Lond. A. 362:1423-1438.
-
(2004)
Philos. Trans. R. Soc. Lond. A
, vol.362
, pp. 1423-1438
-
-
Travers, A.A.1
-
17
-
-
0022413269
-
Analysis of ring-closure probabilities of isotropic worm-like chains: Application to DNA
-
Hagerman, P. J. 1985. Analysis of ring-closure probabilities of isotropic worm-like chains: application to DNA. Biopolymers. 24:1881-1897.
-
(1985)
Biopolymers
, vol.24
, pp. 1881-1897
-
-
Hagerman, P.J.1
-
18
-
-
0026796061
-
DNA bending, flexibility, and helical repeat by cyclization kinetics
-
Crothers, D. M., J. Drak, J. D. Kahn, and S. D. Levene. 1992. DNA bending, flexibility, and helical repeat by cyclization kinetics. Methods Enzymol. 212:3-29.
-
(1992)
Methods Enzymol.
, vol.212
, pp. 3-29
-
-
Crothers, D.M.1
Drak, J.2
Kahn, J.D.3
Levene, S.D.4
-
19
-
-
0028289189
-
Detection of localized DNA flexibility
-
Kahn, J. D., E. Yun, and D. M. Crothers. 1994. Detection of localized DNA flexibility. Nature. 368:163-166.
-
(1994)
Nature
, vol.368
, pp. 163-166
-
-
Kahn, J.D.1
Yun, E.2
Crothers, D.M.3
-
21
-
-
0025366778
-
Dependence of the torsional rigidity of DNA on base composition
-
Fujimoto, B. S., and J. M. Schurr. 1990. Dependence of the torsional rigidity of DNA on base composition. Nature. 344:175-178.
-
(1990)
Nature
, vol.344
, pp. 175-178
-
-
Fujimoto, B.S.1
Schurr, J.M.2
-
22
-
-
85015087906
-
Ten years of tension: Single-molecule DNA mechanics
-
Bustamante, C., Z. Bryant, and S. B. Smith. 2003. Ten years of tension: single-molecule DNA mechanics. Nature. 421:423-426.
-
(2003)
Nature
, vol.421
, pp. 423-426
-
-
Bustamante, C.1
Bryant, Z.2
Smith, S.B.3
-
23
-
-
14244271476
-
Molecular dynamics simulation of nucleic acids: Successes, limitations, and promise
-
Cheatham III, T. E., and M. A. Young. 2001. Molecular dynamics simulation of nucleic acids: successes, limitations, and promise. Biopolymers. 56:232-256.
-
(2001)
Biopolymers
, vol.56
, pp. 232-256
-
-
Cheatham III, T.E.1
Young, M.A.2
-
24
-
-
0036286321
-
Simulations of nucleic acids and their complexes
-
Giudice, E., and R. Lavery. 2002. Simulations of nucleic acids and their complexes. Acc. Chem. Res. 35:350-357.
-
(2002)
Acc. Chem. Res.
, vol.35
, pp. 350-357
-
-
Giudice, E.1
Lavery, R.2
-
25
-
-
4444351490
-
Empirical force fields for biological macromolecules: Overview and issues
-
MacKerell, A. D. 2004. Empirical force fields for biological macromolecules: overview and issues. J. Comput. Chem. 25:1584-1604.
-
(2004)
J. Comput. Chem.
, vol.25
, pp. 1584-1604
-
-
MacKerell, A.D.1
-
26
-
-
2942547665
-
Simulation and modeling of nucleic acid structure, dynamics and interactions
-
Cheatham, T. E. 2004. Simulation and modeling of nucleic acid structure, dynamics and interactions. Curr. Opin. Struct. Biol. 14:360-367.
-
(2004)
Curr. Opin. Struct. Biol.
, vol.14
, pp. 360-367
-
-
Cheatham, T.E.1
-
27
-
-
0031836876
-
Sequence-dependent dynamics of TATA-box binding sites
-
Flatters, D., and R. Lavery. 1998. Sequence-dependent dynamics of TATA-box binding sites. Biophys. J. 75:372-381.
-
(1998)
Biophys. J.
, vol.75
, pp. 372-381
-
-
Flatters, D.1
Lavery, R.2
-
28
-
-
0348244547
-
All-atom empirical force field for nucleic acids. 1. Parameter optimization based on small molecule and condensed phase macromolecular target data
-
Foloppe, N., and A. D. MacKerell. 2000. All-atom empirical force field for nucleic acids. 1. Parameter optimization based on small molecule and condensed phase macromolecular target data. J. Comput. Chem. 21:86-104.
-
(2000)
J. Comput. Chem.
, vol.21
, pp. 86-104
-
-
Foloppe, N.1
MacKerell, A.D.2
-
29
-
-
1242336961
-
DNA sequence-dependent deformability-insights from computer simulations
-
Lankas, F. 2003. DNA sequence-dependent deformability-insights from computer simulations. Biopolymers. 73:327-339.
-
(2003)
Biopolymers
, vol.73
, pp. 327-339
-
-
Lankas, F.1
-
30
-
-
1842607449
-
DNA deformability at the basepair level
-
Lankas, F., J. Sponer, J. Langowski, and T. E. Cheatham. 2003. DNA deformability at the basepair level. J. Am. Chem. Soc. 126:4124-4125.
-
(2003)
J. Am. Chem. Soc.
, vol.126
, pp. 4124-4125
-
-
Lankas, F.1
Sponer, J.2
Langowski, J.3
Cheatham, T.E.4
-
31
-
-
0242290881
-
DNA basepair step deformability inferred from molecular dynamics simulations
-
Lankas, F., J. Sponer, J. Langowski, and T. E. Cheatham. 2004. DNA basepair step deformability inferred from molecular dynamics simulations. Biophys. J. 85:2872-2883.
-
(2004)
Biophys. J.
, vol.85
, pp. 2872-2883
-
-
Lankas, F.1
Sponer, J.2
Langowski, J.3
Cheatham, T.E.4
-
32
-
-
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., G. Barreiro, K. S. Byun, D. A. Case, T. E. Cheatham 3rd, S. B. Dixit, E. Giudice, F. Lankas, R. Lavery, J. H. Maddocks, R. Osman, E. Seibert, H. Sklenar, G. Stoll, K. M. Thayer, P. Varnai, and M. A. Young. 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 III, T.E.5
Dixit, S.B.6
Giudice, E.7
Lankas, F.8
Lavery, R.9
Maddocks, J.H.10
Osman, R.11
Seibert, E.12
Sklenar, H.13
Stoll, G.14
Thayer, K.M.15
Varnai, P.16
Young, M.A.17
-
33
-
-
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., D. L. Beveridge, D. A. Case, T. E. Cheatham III, E. Giudice, F. Lankas, R. Lavery, J. H. Maddocks, R. Osman, H. Sklenar, K. M. Thayer, and P. Varnai. 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 III, T.E.4
Giudice, E.5
Lankas, F.6
Lavery, R.7
Maddocks, J.H.8
Osman, R.9
Sklenar, H.10
Thayer, K.M.11
Varnai, P.12
-
34
-
-
25844459462
-
-
University of California, San Francisco, CA
-
Case, D. A., D. A. Pearlman, J. W. Caldwell, T. E. Cheatham III, W. S. Ross, C. L. Simmerling, T. A. Darden, K. M. Merz, R. V. Stanton, A. L. Cheng, J. J. Vincent, M. Crowley, V. Tsui, R. J. Radmer, Y. Duan, J. Pitera, I. Massova, G. L. Seibel, U. C. Singh, P. K. Weiner, and P. A. Kollman. 2003. AMBER 8. University of California, San Francisco, CA.
-
(2003)
AMBER 8
-
-
Case, D.A.1
Pearlman, D.A.2
Caldwell, J.W.3
Cheatham III, T.E.4
Ross, W.S.5
Simmerling, C.L.6
Darden, T.A.7
Merz, K.M.8
Stanton, R.V.9
Cheng, A.L.10
Vincent, J.J.11
Crowley, M.12
Tsui, V.13
Radmer, R.J.14
Duan, Y.15
Pitera, J.16
Massova, I.17
Seibel, G.L.18
Singh, U.C.19
Weiner, P.K.20
Kollman, P.A.21
more..
-
35
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
Jorgensen, W., J. Chandrasekhar, J. Madura, R. Impey, and M. Klein. 1983. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79:926-935.
-
(1983)
J. Chem. Phys.
, vol.79
, pp. 926-935
-
-
Jorgensen, W.1
Chandrasekhar, J.2
Madura, J.3
Impey, R.4
Klein, M.5
-
36
-
-
0032922174
-
A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat
-
Cheatham III, T. E., P. Cieplak, and P. A. Kollman. 1999. A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat. J. Biomol. Struct. Dyn. 16:845-862.
-
(1999)
J. Biomol. Struct. Dyn.
, vol.16
, pp. 845-862
-
-
Cheatham III, T.E.1
Cieplak, P.2
Kollman, P.A.3
-
37
-
-
0242663237
-
A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations
-
Duan, Y., C. Wu, S. Chowdhury, M. C. Lee, G. Xiong, W. Zhang, R. Yang, P. Cieplak, R. Luo, T. Lee, J. Caldwell, J. Wang, and P. Kollman. 2003. A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. J. Comput. Chem. 24:1999-2012.
-
(2003)
J. Comput. Chem.
, vol.24
, pp. 1999-2012
-
-
Duan, Y.1
Wu, C.2
Chowdhury, S.3
Lee, M.C.4
Xiong, G.5
Zhang, W.6
Yang, R.7
Cieplak, P.8
Luo, R.9
Lee, T.10
Caldwell, J.11
Wang, J.12
Kollman, P.13
-
38
-
-
33846823909
-
Particle mesh Ewald: An NlogN method for Ewald sums in large systems
-
Darden, T. A., D. M. York, and L. Pedersen. 1993. Particle mesh Ewald: an NlogN method for Ewald sums in large systems. J. Chem. Phys. 98:10089-10092.
-
(1993)
J. Chem. Phys.
, vol.98
, pp. 10089-10092
-
-
Darden, T.A.1
York, D.M.2
Pedersen, L.3
-
39
-
-
84986440341
-
SETTLE: An analytical version of the SHAKE and RATTLE algorithm for rigid water models
-
Miyamoto, S., and P. A. Kollman. 1992. SETTLE: an analytical version of the SHAKE and RATTLE algorithm for rigid water models. J. Comput. Chem. 13:952-962.
-
(1992)
J. Comput. Chem.
, vol.13
, pp. 952-962
-
-
Miyamoto, S.1
Kollman, P.A.2
-
40
-
-
0024058085
-
The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids
-
Lavery, R., and H. Sklenar. 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
-
41
-
-
0024539180
-
Defining the structure of irregular nucleic acids: Conventions and principles
-
Lavery, R., and H. Sklenar. 1988. Defining the structure of irregular nucleic acids: conventions and principles. J. Biomol. Struct. Dyn. 6:655-667.
-
(1988)
J. Biomol. Struct. Dyn.
, vol.6
, pp. 655-667
-
-
Lavery, R.1
Sklenar, H.2
-
42
-
-
84986519238
-
The weighted histogram analysis method for free-energy calculations on biomolecules. I. The method
-
Kumar, S., D. Bouzida, R. H. Swendsen, P. A. Kollman, and J. M. Rosenberg. 1992. The weighted histogram analysis method for free-energy calculations on biomolecules. I. The method. J. Comput. Chem. 13:1011-1021.
-
(1992)
J. Comput. Chem.
, vol.13
, pp. 1011-1021
-
-
Kumar, S.1
Bouzida, D.2
Swendsen, R.H.3
Kollman, P.A.4
Rosenberg, J.M.5
-
43
-
-
85030601012
-
-
Grossfield, A. 2003. http://dasher.wustl.edu/alan.
-
(2003)
-
-
Grossfield, A.1
-
44
-
-
0029011701
-
A second generation force field for simulation of proteins, nucleic acids and organic molecules
-
Cornell, W. D., P. Cieplak, C. I. Bayley, I. R. Gould, K. M. Merz, D. M. Ferguson, D. C. Spellmeyer, T. Fox, J. W. Caldwell, and P. A. Kollman. 1995. A second generation force field for simulation of proteins, nucleic acids and organic molecules. J. Am. Chem. Soc. 117:5179-5197.
-
(1995)
J. Am. Chem. Soc.
, vol.117
, pp. 5179-5197
-
-
Cornell, W.D.1
Cieplak, P.2
Bayley, C.I.3
Gould, I.R.4
Merz, K.M.5
Ferguson, D.M.6
Spellmeyer, D.C.7
Fox, T.8
Caldwell, J.W.9
Kollman, P.A.10
-
45
-
-
0034063442
-
Conformational deformability of RNA: A harmonic mode analysis
-
Zacharias, M., and H. Sklenar. 2000. Conformational deformability of RNA: a harmonic mode analysis. Biophys. J. 78:2528-2542.
-
(2000)
Biophys. J.
, vol.78
, pp. 2528-2542
-
-
Zacharias, M.1
Sklenar, H.2
-
46
-
-
0034578639
-
Comparison of molecular dynamics and harmonic mode calculations on RNA
-
Zacharias, M. 2000. Comparison of molecular dynamics and harmonic mode calculations on RNA. Biopolymers. 54:547-560.
-
(2000)
Biopolymers
, vol.54
, pp. 547-560
-
-
Zacharias, M.1
-
47
-
-
24344466194
-
Structural and dynamic effects of single 7-hydro-8-oxoguanine bases located in a frameshift target DNA sequence
-
Barone, F., F. Lankas, N. Spackova, J. Sponer, P. Karran, M. Bignami, and F. Mazzei. 2005. Structural and dynamic effects of single 7-hydro-8-oxoguanine bases located in a frameshift target DNA sequence. Biophys. Chem. 118:31-41.
-
(2005)
Biophys. Chem.
, vol.118
, pp. 31-41
-
-
Barone, F.1
Lankas, F.2
Spackova, N.3
Sponer, J.4
Karran, P.5
Bignami, M.6
Mazzei, F.7
|