-
1
-
-
0016811726
-
Computer analysis of conformational properties of double-helical DNA
-
Zhurkin VB, Lysov YP, Ivanov VI: Computer analysis of conformational properties of double-helical DNA. FEBS Lett 1975, 59:44-47.
-
(1975)
FEBS Lett
, vol.59
, pp. 44-47
-
-
Zhurkin, V.B.1
Lysov, Y.P.2
Ivanov, V.I.3
-
2
-
-
0016803261
-
Investigation of fibrous structures. II. General method for the elucidation of the conformations of the complementary nucleic acids
-
Tumanyan VG, Esipova NG: Investigation of fibrous structures. II. General method for the elucidation of the conformations of the complementary nucleic acids. Biopolymers 1975, 14:2231-2246.
-
(1975)
Biopolymers
, vol.14
, pp. 2231-2246
-
-
Tumanyan, V.G.1
Esipova, N.G.2
-
3
-
-
0018459032
-
Interactions of molecules with nucleic acids. I. An algorithm to generate nucleic acid structures with an application to the B-DNA structure and a counterclockwise helix
-
Miller KJ: Interactions of molecules with nucleic acids. I. An algorithm to generate nucleic acid structures with an application to the B-DNA structure and a counterclockwise helix. Biopolymers 1979, 18:959-980.
-
(1979)
Biopolymers
, vol.18
, pp. 959-980
-
-
Miller, K.J.1
-
5
-
-
0032054952
-
Simulations of the molecular dynamics of nucleic acids
-
Auffinger P, Westhof E: Simulations of the molecular dynamics of nucleic acids. Curr Opin Struct Biol 1998, 8:227-236.
-
(1998)
Curr Opin Struct Biol
, vol.8
, pp. 227-236
-
-
Auffinger, P.1
Westhof, E.2
-
6
-
-
0030919777
-
Construction of double-helical DNA structures based on dinucleotide building blocks
-
Hunter CA, Lu XJ: Construction of double-helical DNA structures based on dinucleotide building blocks. J Biomol Struct Dyn 1997, 14:747-756.
-
(1997)
J Biomol Struct Dyn
, vol.14
, pp. 747-756
-
-
Hunter, C.A.1
Lu, X.J.2
-
7
-
-
0031847234
-
Modeling active RNA structures using the intersection of conformational space: Application to the lead-activated ribozyme
-
Lemieux S, Chartrand P, Cedegren R, Major F: Modeling active RNA structures using the intersection of conformational space: Application to the lead-activated ribozyme. RNA 1998, 4:739-749. The authors describe a method for selecting amongst possible models of folded RNA by checking their compatibility with known experimental data on sequence variants.
-
(1998)
RNA
, vol.4
, pp. 739-749
-
-
Lemieux, S.1
Chartrand, P.2
Cedegren, R.3
Major, F.4
-
8
-
-
0026077710
-
The combination of symbolic and numerical computation for three-dimensional modeling of RNA
-
Major F, Turcotte M, Gautheret D, Lapalme G, Fillion E, Cedergren R: The combination of symbolic and numerical computation for three-dimensional modeling of RNA. Science 1991, 253:1255-1260.
-
(1991)
Science
, vol.253
, pp. 1255-1260
-
-
Major, F.1
Turcotte, M.2
Gautheret, D.3
Lapalme, G.4
Fillion, E.5
Cedergren, R.6
-
9
-
-
0030623530
-
Predicting RNA structures: The model of the RNA element binding Rev meets the NMR structure
-
Leclerc F, Srinivisan J, Cedergren R: Predicting RNA structures: The model of the RNA element binding Rev meets the NMR structure. Fold Des 1997, 2:141-147.
-
(1997)
Fold Des
, vol.2
, pp. 141-147
-
-
Leclerc, F.1
Srinivisan, J.2
Cedergren, R.3
-
10
-
-
0031021456
-
A computational approach to modeling nucleic acid hairpin structure
-
Tung CS: A computational approach to modeling nucleic acid hairpin structure. Biophys J 1997, 72:876-885.
-
(1997)
Biophys J
, vol.72
, pp. 876-885
-
-
Tung, C.S.1
-
12
-
-
0031556948
-
DNA base-stacking interactions: A comparison of theoretical calculations with oligonucleotides X-ray crystal structures
-
Hunter CA, Lu XJ: DNA base-stacking interactions: A comparison of theoretical calculations with oligonucleotides X-ray crystal structures. J Mol Biol 1997, 265:603-619.
-
(1997)
J Mol Biol
, vol.265
, pp. 603-619
-
-
Hunter, C.A.1
Lu, X.J.2
-
13
-
-
0032540859
-
Sequence dependent DNA structure: The role of the sugar-phosphate backbone
-
Packer MJ, Hunter CA: Sequence dependent DNA structure: The role of the sugar-phosphate backbone. J Mol Biol 1998, 280:407-420.
-
(1998)
J Mol Biol
, vol.280
, pp. 407-420
-
-
Packer, M.J.1
Hunter, C.A.2
-
14
-
-
0032573871
-
Molecular models of nucleic acids triple helixes I. DNA and RNA backbone complexes
-
Srinivasan AR, Olson WK: Molecular models of nucleic acids triple helixes I. DNA and RNA backbone complexes. J Am Chem Soc 1998, 120:484-491.
-
(1998)
J Am Chem Soc
, vol.120
, pp. 484-491
-
-
Srinivasan, A.R.1
Olson, W.K.2
-
15
-
-
0032573846
-
Molecular models of nucleic acids triple helixes II. PNA and 2′-5′ backbone complexes
-
Srinivasan AR, Olson WK: Molecular models of nucleic acids triple helixes II. PNA and 2′-5′ backbone complexes. J Am Chem Soc 1998, 120:492-499.
-
(1998)
J Am Chem Soc
, vol.120
, pp. 492-499
-
-
Srinivasan, A.R.1
Olson, W.K.2
-
16
-
-
0030735002
-
Analysis of the stability of looped-out and stacked-in conformations of an adenine bulge in DNA using a continuum model for solvent and ions
-
Zacharias M, Sklenar H: Analysis of the stability of looped-out and stacked-in conformations of an adenine bulge in DNA using a continuum model for solvent and ions. Biophys J 1997, 73:2990-3003.
-
(1997)
Biophys J
, vol.73
, pp. 2990-3003
-
-
Zacharias, M.1
Sklenar, H.2
-
17
-
-
0029286439
-
Triad-DNA: A model for trinucleotide repeats
-
Kuryavyi VV, Jovin TM: Triad-DNA: A model for trinucleotide repeats. Nat Genet 1995, 9:339-341.
-
(1995)
Nat Genet
, vol.9
, pp. 339-341
-
-
Kuryavyi, V.V.1
Jovin, T.M.2
-
18
-
-
0030992537
-
Local DNA stretching mimics the distortion caused by the TATA box-binding protein
-
Lebrun A, Shakked Z, Lavery R: Local DNA stretching mimics the distortion caused by the TATA box-binding protein. Proc Natl Acad Sci USA 1997, 94:2993-2998. The authors show that locally increasing the distance between two phosphate groups at the 3'′ ends of the TBP-binding site leads to minor-groove opening and bending, creating a conformation that is very like that induced by the protein.
-
(1997)
Proc Natl Acad Sci USA
, vol.94
, pp. 2993-2998
-
-
Lebrun, A.1
Shakked, Z.2
Lavery, R.3
-
19
-
-
0033561745
-
Modeling DNA deformations induced by minor groove binding proteins
-
in press
-
Lebrun A, Lavery R: Modeling DNA deformations induced by minor groove binding proteins. Biopolymers 1999, in press.
-
(1999)
Biopolymers
-
-
Lebrun, A.1
Lavery, R.2
-
20
-
-
0030915267
-
Architectural accommodation in the complex of four p53 DNA binding domain peptides with the p21/waf1/cip1 DNA response element
-
Nagaich AK, Zhurkin VB, Sakamoto H, Gorin AA, Clore GM, Gronenborn AM, Appella E, Harrington RE: Architectural accommodation in the complex of four p53 DNA binding domain peptides with the p21/waf1/cip1 DNA response element. J Biol Chem 1997, 272:14830-14841. In accord with cyclisation data, simplified modelling of the p53 tetramer complex with DNA suggests that the target site must bend by roughly 50° in order to avoid clashes between the protein subunits.
-
(1997)
J Biol Chem
, vol.272
, pp. 14830-14841
-
-
Nagaich, A.K.1
Zhurkin, V.B.2
Sakamoto, H.3
Gorin, A.A.4
Clore, G.M.5
Gronenborn, A.M.6
Appella, E.7
Harrington, R.E.8
-
21
-
-
0000075293
-
DNA bending induced by tetrameric binding of the p53 tumor suppresser protein: Steric constraints on conformation
-
Edited by Sarma RH, Sarma MH. New York: Adenine Press
-
Durell SR, Jernigan RL, Appella E, Nagaich AK, Harrington RE, Zhurkin VB: DNA bending induced by tetrameric binding of the p53 tumor suppresser protein: Steric constraints on conformation. In Structure, Motion, Interaction and Expression of Biological Macromolecule. Proceedings of the Tenth Conversation. Edited by Sarma RH, Sarma MH. New York: Adenine Press; 1998:277-295.
-
(1998)
Structure, Motion, Interaction and Expression of Biological Macromolecule. Proceedings of the Tenth Conversation
, pp. 277-295
-
-
Durell, S.R.1
Jernigan, R.L.2
Appella, E.3
Nagaich, A.K.4
Harrington, R.E.5
Zhurkin, V.B.6
-
22
-
-
84986495504
-
Small amplitude protein conformational dynamics: Second-order analytic relation between Cartesian coordinates and dihedral angles
-
Sunada S, Go N: Small amplitude protein conformational dynamics: second-order analytic relation between Cartesian coordinates and dihedral angles. J Comput Chem 1995, 16:328-336.
-
(1995)
J Comput Chem
, vol.16
, pp. 328-336
-
-
Sunada, S.1
Go, N.2
-
23
-
-
0000213488
-
Calculation and analysis of low-frequency normal modes for DNA
-
Ha Duong T, Zakrzewska K: Calculation and analysis of low-frequency normal modes for DNA. J Comput Chem 1997, 18:796-811.
-
(1997)
J Comput Chem
, vol.18
, pp. 796-811
-
-
Ha Duong, T.1
Zakrzewska, K.2
-
24
-
-
0032479181
-
Sequence specificity of bacteriophage 434 repressor-operator complexation
-
Ha Duong T, Zakrzewska K: Sequence specificity of bacteriophage 434 repressor-operator complexation. J Mol Biol 1998, 280:31-39.
-
(1998)
J Mol Biol
, vol.280
, pp. 31-39
-
-
Ha Duong, T.1
Zakrzewska, K.2
-
25
-
-
0345326630
-
DNA curvature and phosphate neutralisation: An important aspect of specific protein binding
-
in press
-
Gurlie R, Zakrzewska K: DNA curvature and phosphate neutralisation: An important aspect of specific protein binding. J Biomol Struct Dyn 1999, in press. Neutralising the phosphate groups involved in salt bridges with cationic sidechains of bound proteins often leads to bending. This study reveals that sliding the neutralisation 'pattern' along the DNA, however, shows that this effect is strongly sequence dependent.
-
(1999)
J Biomol Struct Dyn
-
-
Gurlie, R.1
Zakrzewska, K.2
-
26
-
-
0009737677
-
Collective variable Monte Carlo simulation of DNA
-
Gabb HA, Prevost C, Bertuckt G, Robert CH, Lavery R: Collective variable Monte Carlo simulation of DNA. J Comput Chem 1997, 18:2001-2011.
-
(1997)
J Comput Chem
, vol.18
, pp. 2001-2011
-
-
Gabb, H.A.1
Prevost, C.2
Bertuckt, G.3
Robert, C.H.4
Lavery, R.5
-
27
-
-
0022036264
-
Efficient Monte Carlo method for simulation of fluctuating conformations of native proteins
-
Noguti T, Go N: Efficient Monte Carlo method for simulation of fluctuating conformations of native proteins. Biopolymers 1985, 24:527-546.
-
(1985)
Biopolymers
, vol.24
, pp. 527-546
-
-
Noguti, T.1
Go, N.2
-
28
-
-
0030621858
-
Torsion-angle molecular dynamics as a new efficient tool for NMR structure calculation
-
Stein EG, Rice LM, Brünger AT: Torsion-angle molecular dynamics as a new efficient tool for NMR structure calculation. J Magn Res 1997, 124:154-164.
-
(1997)
J Magn Res
, vol.124
, pp. 154-164
-
-
Stein, E.G.1
Rice, L.M.2
Brünger, A.T.3
-
29
-
-
0031576336
-
Torsion angle dynamics for NMR structure calculation with the new program DYANA
-
Guntert P, Mumenthaler C, Wüthrich K: Torsion angle dynamics for NMR structure calculation with the new program DYANA. J Mol Biol 1997, 273:283-298.
-
(1997)
J Mol Biol
, vol.273
, pp. 283-298
-
-
Guntert, P.1
Mumenthaler, C.2
Wüthrich, K.3
-
30
-
-
0030918784
-
Chirality errors in nucleic acid structures
-
Schultze P, Feigon J: Chirality errors in nucleic acid structures. Nature 1997, 387:668.
-
(1997)
Nature
, vol.387
, pp. 668
-
-
Schultze, P.1
Feigon, J.2
-
31
-
-
0032576192
-
Accurate DNA dynamics without accurate long range electrostatics
-
Mazur AK: Accurate DNA dynamics without accurate long range electrostatics. J Am Chem Soc 1998, 120:10928-10937. The approach proposed by the author enables stable multinanosecond trajectories of DNA oligomers to be obtained using internal coordinates and a time step of 10 fs. The results, which model solvent using a hybrid discrete/continuum model, yield conformations close to crystallographic data.
-
(1998)
J Am Chem Soc
, vol.120
, pp. 10928-10937
-
-
Mazur, A.K.1
-
32
-
-
0030064676
-
DNA: An extensible molecule
-
Cluzel P, Lebrun A, Heller C, Lavery R, Viovy JL, Chatenay D, Caron F: DNA: An extensible molecule. Science 1996, 271:791 -794.
-
(1996)
Science
, vol.271
, pp. 791-794
-
-
Cluzel, P.1
Lebrun, A.2
Heller, C.3
Lavery, R.4
Viovy, J.L.5
Chatenay, D.6
Caron, F.7
-
33
-
-
0030024985
-
Overstretching B-DNA: The elastic response of individual double-stranded and single-stranded DNA molecules
-
Smith SB, Cui Y, Bustamante C: Overstretching B-DNA: The elastic response of individual double-stranded and single-stranded DNA molecules. Science 1996, 271:795-799.
-
(1996)
Science
, vol.271
, pp. 795-799
-
-
Smith, S.B.1
Cui, Y.2
Bustamante, C.3
-
34
-
-
0031194539
-
Stretching and breaking duplex DNA by chemical force microscopy
-
Noy A, Vezenov DV, Kayyem JF, Meade TJ, Lieber CM: Stretching and breaking duplex DNA by chemical force microscopy. Chem Biol 1997, 4:519-527.
-
(1997)
Chem Biol
, vol.4
, pp. 519-527
-
-
Noy, A.1
Vezenov, D.V.2
Kayyem, J.F.3
Meade, T.J.4
Lieber, C.M.5
-
35
-
-
0009695951
-
Modeling the mechanics of a DNA oligomer
-
in press
-
Lebrun A, Lavery R: Modeling the mechanics of a DNA oligomer. J Biomol Struct Dyn 1999, in press.
-
(1999)
J Biomol Struct Dyn
-
-
Lebrun, A.1
Lavery, R.2
-
37
-
-
0032468201
-
A model for parallel triple helix formation by RecA: Single-strand association with a homologous duplex via the major groove
-
Bertucat G, Lavery R, Prevost C: A model for parallel triple helix formation by RecA: Single-strand association with a homologous duplex via the major groove. J Biomol Struct Dyn 1998, 16:1-13. This paper reports how stretching the 3′ ends of DNA opens the minor groove sufficiently to allow complexation with a single-stranded DNA-RecA filament and suggests that strand exchange may occur by base rotation, leading to a leaving strand situated on the major groove.
-
(1998)
J Biomol Struct Dyn
, vol.16
, pp. 1-13
-
-
Bertucat, G.1
Lavery, R.2
Prevost, C.3
-
38
-
-
0032530848
-
Base pair switching by interconversion of sugar puckers in DNA extended by proteins of RecA-family: A model for homology search in homologous genetic recombination
-
Nichinaka T, Shinohara A, Ito Y, Yokoyama S, Shibata T: Base pair switching by interconversion of sugar puckers in DNA extended by proteins of RecA-family: A model for homology search in homologous genetic recombination. Proc Natl Acad Sci USA 1998, 95:11071-11076. The authors describe a very similar model to that mentioned in [37•], based on NMR data for a RecA-dinucleotide complex. This mechanism stresses the importance of sugar pucker changes.
-
(1998)
Proc Natl Acad Sci USA
, vol.95
, pp. 11071-11076
-
-
Nichinaka, T.1
Shinohara, A.2
Ito, Y.3
Yokoyama, S.4
Shibata, T.5
-
39
-
-
0032564447
-
Stretched and overwound DNA forms a Pauling-like structure with exposed bases
-
Allemand JF, Bensimon D, Lavery R, Croquette V: Stretched and overwound DNA forms a Pauling-like structure with exposed bases. Proc Natl Acad Sci USA 1998, 95:14152-14157. Positive supercoiling of stretched DNA leads to base-pair breaking and transition to a conformation with the phosphodiester backbones inside and the bases outside. A similar structure has already been proposed to exist within a filamentous bacteriophage [66].
-
(1998)
Proc Natl Acad Sci USA
, vol.95
, pp. 14152-14157
-
-
Allemand, J.F.1
Bensimon, D.2
Lavery, R.3
Croquette, V.4
-
40
-
-
0002572036
-
A proposed structure for the nucleic acids
-
Pauling L, Corey RB: A proposed structure for the nucleic acids. Proc Natl Acad Sci USA 1953, 39:84-96.
-
(1953)
Proc Natl Acad Sci USA
, vol.39
, pp. 84-96
-
-
Pauling, L.1
Corey, R.B.2
-
41
-
-
0030729494
-
Search for rigid subdomains in DNA from molecular dynamics simulations
-
Gaudin F, Lancelot G, Genest D: Search for rigid subdomains in DNA from molecular dynamics simulations. J Biomol Struct Dyn 1997, 15:357-367. This paper describes a method for finding the atoms of DNA that can be grouped into rigid bodies for a given error in the root mean square fluctuations of interatomic distances derived from all-atom dynamic trajectories.
-
(1997)
J Biomol Struct Dyn
, vol.15
, pp. 357-367
-
-
Gaudin, F.1
Lancelot, G.2
Genest, D.3
-
42
-
-
0030733693
-
Simulation of the conformation and dynamics of a double-helical model for DNA
-
Huertas ML, Navarro S, Lopez Martinez MC, Garcia de la Torre G: Simulation of the conformation and dynamics of a double-helical model for DNA. Biophys J 1997, 73:3142-3143.
-
(1997)
Biophys J
, vol.73
, pp. 3142-3143
-
-
Huertas, M.L.1
Navarro, S.2
Lopez Martinez, M.C.3
Garcia De La Torre, G.4
-
43
-
-
0031559721
-
Modeling self contact forces in the elastic theory of DNA supercoiling
-
Westcott TP, Tobias I, Olson WK: Modeling self contact forces in the elastic theory of DNA supercoiling. J Chem Phys 1997, 107:3967-3980.
-
(1997)
J Chem Phys
, vol.107
, pp. 3967-3980
-
-
Westcott, T.P.1
Tobias, I.2
Olson, W.K.3
-
44
-
-
0032168436
-
Rod models of DNA: Sequence-dependent anisotropic elastic modelling of local phenomena
-
Munteanu MG, Vlahovicek K, Parthasarathy S, Simon I, Pongor S: Rod models of DNA: Sequence-dependent anisotropic elastic modelling of local phenomena. Trends Biochem Sci 1998, 23:341-346. This paper describes a segmented rod model of DNA that only bends towards the major groove at each step and includes sequence-dependent flexibility based on nuclease digestion results.
-
(1998)
Trends Biochem Sci
, vol.23
, pp. 341-346
-
-
Munteanu, M.G.1
Vlahovicek, K.2
Parthasarathy, S.3
Simon, I.4
Pongor, S.5
-
45
-
-
0031048190
-
The effect of intrinsic curvature on conformational properties of circular DNA
-
Katritch V, Vologodskii AV: The effect of intrinsic curvature on conformational properties of circular DNA. Biophys J 1997, 72:1070-1079. A dinucleotide wedge model of DNA bending was used to build a segmented rod model including averaged sequence effects. The results of Monte Carlo simulations show that intrinsic curvature can strongly influence the equilibrium distribution of linking number for circular DNAs of roughly 300-1000 base pairs.
-
(1997)
Biophys J
, vol.72
, pp. 1070-1079
-
-
Katritch, V.1
Vologodskii, A.V.2
-
46
-
-
0031969344
-
The elastic rod model for DNA and its application to the tertiary structure of DNA minicircles in mononucleosomes
-
Swigon D, Coleman BD, Tobias I: The elastic rod model for DNA and its application to the tertiary structure of DNA minicircles in mononucleosomes. Biophys J 1998, 74:2515-2530.
-
(1998)
Biophys J
, vol.74
, pp. 2515-2530
-
-
Swigon, D.1
Coleman, B.D.2
Tobias, I.3
-
47
-
-
0030005131
-
Simulating DNA at low resolution
-
Olson WK: Simulating DNA at low resolution. Curr Opin Struct Biol 1996, 6:242-256.
-
(1996)
Curr Opin Struct Biol
, vol.6
, pp. 242-256
-
-
Olson, W.K.1
-
48
-
-
0029066852
-
Modeling superhelical DNA: Recent analytical and dynamic approaches
-
Schlick T: Modeling superhelical DNA: Recent analytical and dynamic approaches. Curr Opin Struct Biol 1995, 5:245-262.
-
(1995)
Curr Opin Struct Biol
, vol.5
, pp. 245-262
-
-
Schlick, T.1
-
49
-
-
0031880233
-
A Brownian dynamics program for the simulation of linear and circular DNA and other wormlike chain polyelectrolytes
-
Klenin KV, Merlitz H, Langowski J: A Brownian dynamics program for the simulation of linear and circular DNA and other wormlike chain polyelectrolytes. Biophys J 1998, 74:780-788.
-
(1998)
Biophys J
, vol.74
, pp. 780-788
-
-
Klenin, K.V.1
Merlitz, H.2
Langowski, J.3
-
50
-
-
0031880930
-
Looping dynamics of linear DNA molecules and the effect of DNA curvature: A study by Brownian dynamics simulation
-
Merlitz H, Rippe K, Klenin KV, Langowski J: Looping dynamics of linear DNA molecules and the effect of DNA curvature: A study by Brownian dynamics simulation. Biophys J 1998, 74:773-779.
-
(1998)
Biophys J
, vol.74
, pp. 773-779
-
-
Merlitz, H.1
Rippe, K.2
Klenin, K.V.3
Langowski, J.4
-
51
-
-
0032573605
-
Internal motion of supercoiled DNA: Brownian dynamics simulations of site juxtaposition
-
Jian H, Schlick T, Vologodskii A: Internal motion of supercoiled DNA: Brownian dynamics simulations of site juxtaposition. J Mol Biol 1998, 284:287-296.
-
(1998)
J Mol Biol
, vol.284
, pp. 287-296
-
-
Jian, H.1
Schlick, T.2
Vologodskii, A.3
-
52
-
-
0030973367
-
Extension of torsionally stressed DNA by external force
-
Vologodskii AV, Marko JF: Extension of torsionally stressed DNA by external force. Biophys J 1997, 73:123-132.
-
(1997)
Biophys J
, vol.73
, pp. 123-132
-
-
Vologodskii, A.V.1
Marko, J.F.2
-
53
-
-
0029937922
-
The elasticity of a single supercoiled DNA molecule
-
Strick TR, Allemand JF, Bensimon D, Bensimon A, Croquette V: The elasticity of a single supercoiled DNA molecule. Science 1996, 271:1835-1837.
-
(1996)
Science
, vol.271
, pp. 1835-1837
-
-
Strick, T.R.1
Allemand, J.F.2
Bensimon, D.3
Bensimon, A.4
Croquette, V.5
-
54
-
-
11744306627
-
Elasticity model of a supercoiled DNA molecule
-
Bouchiat C, Mézard M: Elasticity model of a supercoiled DNA molecule. Phys Rev Lett 1998, 80:1556-1559.
-
(1998)
Phys Rev Lett
, vol.80
, pp. 1556-1559
-
-
Bouchiat, C.1
Mézard, M.2
-
55
-
-
0032479186
-
Polymer chain statistics and conformational analysis of DNA molecules with bends or sections of different flexibility
-
Rivetti C, Walker C, Bustamante C: Polymer chain statistics and conformational analysis of DNA molecules with bends or sections of different flexibility. J Mol Biol 1998, 280:41 -59.
-
(1998)
J Mol Biol
, vol.280
, pp. 41-59
-
-
Rivetti, C.1
Walker, C.2
Bustamante, C.3
-
56
-
-
0030825156
-
Configurational transitions in Fourier series-represented DNA supercoils
-
Liu GH, Schlick T, Olson AJ, Olson WK: Configurational transitions in Fourier series-represented DNA supercoils. Biophys J 1997, 73:1742-1762. A reduced variable representation of circular DNA elastic rods that improves on earlier B-spline models is described.
-
(1997)
Biophys J
, vol.73
, pp. 1742-1762
-
-
Liu, G.H.1
Schlick, T.2
Olson, A.J.3
Olson, W.K.4
-
57
-
-
0031967830
-
Modeling chain folding in protein-constrained circular DNA
-
Martino JA, Olson WK: Modeling chain folding in protein- constrained circular DNA. Biophys J 1998, 74:2491-2500.
-
(1998)
Biophys J
, vol.74
, pp. 2491-2500
-
-
Martino, J.A.1
Olson, W.K.2
-
58
-
-
0030916931
-
A Brownian dynamics model for the chromatin fiber
-
Ehrlich L, Münkel C, Chirico G, Langowski J: A Brownian dynamics model for the chromatin fiber. CABIOS 1997, 13:271-279.
-
(1997)
CABIOS
, vol.13
, pp. 271-279
-
-
Ehrlich, L.1
Münkel, C.2
Chirico, G.3
Langowski, J.4
-
59
-
-
0031234623
-
A combined wormlike-chain and bead model for dynamic simulations of long linear DNA
-
Jian H, Vologodskii AV, Schlick T: A combined wormlike-chain and bead model for dynamic simulations of long linear DNA. J Comput Phys 1997, 136:168-179. The authors extended the worm-like chain model for DNA by the addition of beads, as well as stretching and electrostatic interactions. Brownian dynamics simulations lead to results that are in good agreement with experimental hydrodynamic data.
-
(1997)
J Comput Phys
, vol.136
, pp. 168-179
-
-
Jian, H.1
Vologodskii, A.V.2
Schlick, T.3
-
60
-
-
0031976753
-
Remarks on discrete and continuous large-scale models of DNA dynamics
-
Klapper I, Qian H: Remarks on discrete and continuous large-scale models of DNA dynamics. Biophys J 1998, 74:2504-2514. A mathematical analysis points to an inconsistency between discrete and continuous models of DNA bending. This implies that an extra tension-like term needs to be added to the limiting case of discrete models to obtain compatible energy expressions.
-
(1998)
Biophys J
, vol.74
, pp. 2504-2514
-
-
Klapper, I.1
Qian, H.2
-
61
-
-
0032072415
-
Chromosome structure predicted by a polymer model
-
Münkel C, Langowski J: Chromosome structure predicted by a polymer model. Phys Rev E 1998, 57:5888-5896. A dynamic simulation of a chromatin fibre using a 'multiloop subcompartment' model based on linked loops composed of rod segments is described.
-
(1998)
Phys Rev E
, vol.57
, pp. 5888-5896
-
-
Münkel, C.1
Langowski, J.2
-
62
-
-
0032480044
-
Chromatin structure and chromosome aberrations: Modeling of damage induced by isotropic and localized irradiation
-
Kreth G, Münkel C, Langowski J, Cremer T, Cremer C: Chromatin structure and chromosome aberrations: Modeling of damage induced by isotropic and localized irradiation. Mutat Res 1998, 404:77-88.
-
(1998)
Mutat Res
, vol.404
, pp. 77-88
-
-
Kreth, G.1
Münkel, C.2
Langowski, J.3
Cremer, T.4
Cremer, C.5
-
63
-
-
0346614808
-
Molecular modeling studies on the ribosome
-
Edited by Leontis NB, SantaLucia J Jr. Washington DC: American Chemical Society
-
Harvey SC, VanLoock MS, Rasterwood TR, Tan RKZ: Molecular modeling studies on the ribosome. In Molecular Modeling of Nucleic Acids. ACS Symposium 682. Edited by Leontis NB, SantaLucia J Jr. Washington DC: American Chemical Society; 1998:369-378.
-
(1998)
Molecular Modeling of Nucleic Acids. ACS Symposium 682
, pp. 369-378
-
-
Harvey, S.C.1
VanLoock, M.S.2
Rasterwood, T.R.3
Tan, R.K.Z.4
-
64
-
-
0033525065
-
Major groove binding of the tRNA/mRNA complex to the 16S ribosomal RNA decoding site
-
Vanloock MS, Easterwood TR, Harvey SC: Major groove binding of the tRNA/mRna complex to the 16S ribosomal RNA decoding site. J Mol Biol 1999, 285:2069-2078.
-
(1999)
J Mol Biol
, vol.285
, pp. 2069-2078
-
-
Vanloock, M.S.1
Easterwood, T.R.2
Harvey, S.C.3
-
65
-
-
0032484151
-
Solution conformations and thermodynamics of structured peptides: Molecular dynamics simulation with an implicit solution model
-
Schaefer M, Bartels C, Karplus M: Solution conformations and thermodynamics of structured peptides: Molecular dynamics simulation with an implicit solution model. J Mol Biol 1998, 284:835-848. Dynamics of two small peptides using the ACE continuum solvent model and the CHARMm force-field were shown to lead to folded conformations that are compatible with NMR data. Poor results are obtained using distance-dependent dielectric functions.
-
(1998)
J Mol Biol
, vol.284
, pp. 835-848
-
-
Schaefer, M.1
Bartels, C.2
Karplus, M.3
-
66
-
-
0028108799
-
Pf1 virus structure: Helical coat protein and DNA with paraxial phosphates
-
Liu DJ, Day LA: Pf1 virus structure: Helical coat protein and DNA with paraxial phosphates. Science 1994, 265:671-674.
-
(1994)
Science
, vol.265
, pp. 671-674
-
-
Liu, D.J.1
Day, L.A.2
|