Molecular dynamics applied to nucleic acids

Accounts of Chemical Research

Volumn 35, Issue 6, 2002, Pages 465-472

  Norberg, Jan ^a   Nilsson, Lennart ^a  

^a KAROLINSKA INSTITUTE   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEIC ACID; OLIGONUCLEOTIDE; RNA; SINGLE STRANDED DNA; PEPTIDE NUCLEIC ACID;

ARTICLE; CONFORMATIONAL TRANSITION; ELECTRICITY; ENERGY; MOLECULAR DYNAMICS; NUCLEIC ACID STRUCTURE; SOLVATION; SURFACE PROPERTY; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; CONFORMATION; MOTION; REVIEW; SOLUBILITY;

COMPUTER SIMULATION; MODELS, MOLECULAR; MOTION; NUCLEIC ACID CONFORMATION; NUCLEIC ACIDS; PEPTIDE NUCLEIC ACIDS; SOLUBILITY;

EID: 0036280718     PISSN: 00014842     EISSN: None     Source Type: Journal    
DOI: 10.1021/ar010026a     Document Type: Article

References (78)

1. Dynamics of folded proteins
2. Computer simulation of DNA double helix dynamics
3. Dynamics of DNA oligomers
4. Molecular dynamics of phenylalanine transfer RNA
5. Structure and dynamics of a fluorescent DNA oligomer containing the EcoRI recognition sequence: Fluorescence, molecular dynamics, and NMR studies
6. Molecular dynamics simulation of the anticodon arm of phenylalanine transfer RNA
7. A molecular dynamics simulation of double helical B-DNA including counterions and water
8. Simulations of the molecular dynamics of nucleic acids
9. Nucleic acids: Theory and computer simulation, Y2K
10. Molecular dynamics simulation of nucleic acids
11. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules
12. All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data
13. Structure, thermodynamics and cooperativity of the glucocorticoid receptor DNA-binding domain in complex with different response elements-molecular dynamics simulation and free energy perturbation studies
14. Interaction of human SRY protein with DNA: A molecular dynamics study
15. Molecular dynamics simulations of the complex between human U1A protein and hairpin II of U1 small nuclear RNA and of free RNA in solution
16. Effect of G40R mutation on the binding of human SRY protein to DNA: A molecular dynamics view
17. Nuclear receptor-DNA binding specificity: A COMBINE and Free-Wilson QSAR analysis
18. Structure, interaction, dynamics and solvent effects on the DNA-EcoRI complex in aqueous solution from molecular dynamics simulation
19. Free energy calculations and molecular dynamics simulations of wild-type and variants of the DNA-EcoRI complex
20. Structural and dynamic differences of the estrogen receptor DNA-binding domain, binding as a dimer and as a monomer to DNA: Molecular dynamics simulation studies
21. Structural and dynamic effects of point mutations in the recognition helix of the glucocorticoid receptor DNA-binding domain
22. Stacking-unstacking of the dinucleoside monophosphate guanylyl-3′,5′-uridine studied with molecular dynamics
23. High-pressure molecular dynamics of a nucleic acid fragment
24. The role of water structure in conformational changes of nucleic acids in ambient and high-pressure conditions
25. Accurate crystal molecular dynamics simulations using particle-mesh-Ewald: RNA dinucleotides-ApU and GpC
26. Stacking free energy profiles for all 16 natural ribodinucleoside monophosphates in aqueous solution
27. Potential of mean force calculations of the stacking unstacking process in single-stranded deoxyribodi-nucleoside monophosphates
28. Temperature dependence of the stacking propensity of adenylyl-3′,5′-adenosine
29. Structure and dynamics of MMI linked nucleotides
30. Conformational analysis of GpA and GpAp in aqueous solution by molecular dynamics and statistical methods
31. Conformational free energy landscape of ApApA from molecular dynamics simulations
32. Influence of adjacent bases on the stacking-unstacking process of single-stranded oligonucleotides
33. Solvent influence on base stacking
34. The structure of a stable intermediate in the A ↔ B DNA helix transition
35. Structure of a B-DNA dodecamer. III. Geometry of hydration
36. Intrinsic conformational properties of Deoxyribonucleosides: Implicated role for cytosine in the equilibrium among the A, B, and Z forms of DNA
37. DNA structure: What's in charge?
38. Flexible structure of DNA: Ion dependence of minor-groove structure and dynamics
39. All-atom empirical force field for nucleic acids: II. Application to molecular dynamics simulations of DNA and RNA in solution
40. Glass transition in DNA from molecular dynamics simulations
41. Structure and hydration of BamHI DNA recognition site: A molecular dynamics investigation
42. A-tract bending: Insight into experimental structures by computational models
43. Dynamic simulations of 13 TATA variants refine kinetic hypotheses of sequence/activity relationships
44. Conformations of an adenine bulge in a DNA octamer and its influence on DNA structure from molecular dynamics simulations
45. Nanosecond molecular dynamics of zipper-like DNA duplex structures containing sheared G-A mismatch pairs
46. 2 in aqueous solution from molecular dynamics simulations
47. 2: A comparison of NMR relaxation measurements with a molecular dynamics simulation
48. Molecular dynamics simulation of DNA stretching is consistent with the tension observed for extension and strand separation and predicts a novel ladder structure
49. Structure, force, and energy of a double-stranded DNA oligonucleotide under tensile loads
50. 2
51. Molecular dynamics simulation reveals conformational switching of water mediated uracil-cytosine base-pairs in an RNA duplex
52. Water ion binding around RNA and DNA (C, G) Oligomers
53. 12 duplexes
54. Molecular dynamics of RNA with the OPLS force field. Aqueous simulation of a hairpin containing a tetranucleotide loop
55. Conformational dynamics of a 5S rRNA hairpin domain containing loop D and a single nucleotide bulge
56. Theoretical studies of an exceptionally stable RNA tetraloop: Observation of convergence from an incorrect NMR structure to the correct one using unrestrained molecular dynamics
57. Continuum solvent studies of the stability of RNA hairpin loops and helices
58. Combined locally enhanced sampling and particle mesh ewald as a strategy to locate the experimental structure of a nonhelical nucleic acid
59. Experimental and theoretical studies of the effects of deoxyribose substitutions on the stability of the UUCG tetraloop
60. Asp anticodon hairpin
61. Phe: Codon-anticodon interaction
62. Wild-type RNA microhelix ala and 3:70 variants: Molecular dynamics analysis of local helical structure and tightly bound water
63. Ala variants
64. Asp
65. Molecular dynamics investigations of hammerhead ribozyme RNA
66. Capturing the structure of a catalytic RNA intermediate: The hammerhead ribozyme
67. Evidence for a hydroxide ion bridging two magnesium ions at the active site of the hammerhead ribozyme
68. Molecular dynamics study displays near in-line attack conformations in the hammerhead ribozyme self-cleavage reaction
69. MD simulations of homomorphous PNA, DNA and RNA single strands: Characterization and comparison of conformations and dynamics
70. Molecular dynamics of duplex systems involving PNA: Structural and dynamical consequences of the nucleic acid backbone
71. Molecular dynamics simulations of PNA-DNA and PNA-RNA duplexes in aqueous solution
72. Molecular dynamics simulation of a PNA-DNA-PNA triple helix in aqueous solution
73. Treatment of electrostatic effects in macromolecular modeling
74. Molecular dynamics simulations of biomolecules: Long-range electrostatic effects
75. New spherical-cutoff methods for long-range forces in macromolecular simulation
76. On the truncation of long-range electrostatic interactions in DNA
77. Ewald artifacts in computer simulations of ionic solvation and ion-ion interaction: A coninuum electrostatics study