10.1016/s0959-440x(96)80046-7
Crossref journal-article
Elsevier BV
Current Opinion in Structural Biology (78)
Bibliography

Louise-May, S., Auffinger, P., & Westhof, E. (1996). Calculations of nucleic acid conformations. Current Opinion in Structural Biology, 6(3), 289–298.

Authors 3
  1. Shirley Louise-May (first)
  2. Pascal Auffinger (additional)
  3. Eric Westhof (additional)
References 89 Referenced 83
  1. 10.1080/07391102.1994.10508746 / J Biomol Struct Dyn / Geometries, charges, dipole moments and interaction energies of normal, tautomeric and novel bases by Jiang (1994)
  2. 10.1021/ja00085a033 / J Am Chem Soc / Theoretical investigation of the hydrogen bond strengths in guanine—cytosine and adenine—thymine base pairs by Gould (1994)
  3. 10.1002/jcc.540161106 / J Comput Chem / Application of the multimolecule and multiconfigurational RESP methodology to biopolymers: charge derivation for DNA, RNA, and proteins by Cieplak (1995)
  4. 10.1021/ja00124a002 / J Am Chem Soc / A second generation force field for the simulation of proteins, nucleic acids, and organic molecules by Cornell (1995)
  5. 10.1021/ja00107a023 / J Am Chem Soc / H-bonded and stacked base pairs: cytosine dimer. An ab initio second order Moller—Plesset study by Hobza (1995)
  6. 10.1002/jcc.540161206 / J Comput Chem / Calculation of molecular geometries, relative conformational energies, dipole moments, and molecular electrostatic fitted charges of small organic molecules of biochemical interest by density functional theory by St. Amant (1995)
  7. 10.1002/(SICI)1096-987X(19960115)17:1<87::AID-JCC8>3.0.CO;2-X / J Comput Chem / Semiemperical treatment of electrostatic potentials and partial charges in combined quantum mechanical and molecular mechanical approaches by Bakowies (1996)
  8. 10.1021/j100048a006 / J Phys Chem / An examination of a Hartree—Fock/molecular mechanical coupled potential by Stanton (1995)
  9. 10.1021/ja00121a029 / J Am Chem Soc / Combined quantum and molecular mechanical study of DNA cross-linking by nitrous acid by Elcock (1995)
  10. 10.1021/j100029a042 / J Phys Chem / Counterion distribution around DNA studied by molecular dynamics and quantum mechanical simulations by Laughton (1995)
  11. 10.1021/ja00149a006 / J Am Chem Soc / Stacking free energy profiles for all 16 natural ribodinucleoside monophosphates in aqueous solution by Norberg (1995)
  12. 10.1016/S0006-3495(95)80098-6 / Biophys J / Potential of mean force calculations of the stacking—unstacking process in single stranded deoxyribonucleoside monophosphates by Norberg (1995)
  13. 10.1021/bi00176a038 / Biochemistry / Contributions of the thymine methyl group to the specific recognition of poly- and mononucleotides: an analysis of the relative free energies of solvation of thymine and uracil by Plaxco (1994)
  14. {'key': '10.1016/S0959-440X(96)80046-7_BIB14', 'first-page': '69', 'article-title': 'Modelling nucleic acids: fine structure, flexibility, and conformational transitions', 'author': 'Lavery', 'year': '1994'} / Modelling nucleic acids: fine structure, flexibility, and conformational transitions by Lavery (1994)
  15. 10.1016/0301-4622(94)85018-6 / Biophys Chem / Modelling DNA conformational mechanics by Lavery (1994)
  16. 10.1002/bip.360340305 / Biopolymers / Measuring the geometry of DNA grooves by Stofer (1994)
  17. {'key': '10.1016/S0959-440X(96)80046-7_BIB17', 'first-page': '103', 'article-title': 'The use of molecular dynamics simulations for modelling nucleic acids', 'author': 'Westhof', 'year': '1995'} / The use of molecular dynamics simulations for modelling nucleic acids by Westhof (1995)
  18. 10.1021/ja00130a011 / J Am Chem Soc / Multiple molecular dynamics simulations of the anticodon loop of tRNAAsp in aqueous solution with counterions by Auffinger (1995)
  19. 10.1016/0009-2614(95)00065-C / Chem Phys Lett / A simple test for evaluating the truncation effects in simulation of systems involving charged groups by Auffinger (1995)
  20. {'key': '10.1016/S0959-440X(96)80046-7_BIB20_1', 'first-page': '1', 'article-title': 'RNA structure from molecular dynamics simulations', 'author': 'Louise-May', 'year': '1995'} / RNA structure from molecular dynamics simulations by Louise-May (1995)
  21. 10.1021/ja952494j / J Am Chem Soc / Molecular dynamics simulations of the anticodon hairpin of tRNAAsp-, structuring effects of CHO hydrogen bonds and of long-range hydration forces by Auffinger (1996)
  22. 10.1063/1.464397 / J Chem Phys / Particle mesh Ewald: an N.log(N) method for Ewald sums in large systems by Darden (1993)
  23. 10.1063/1.470117 / J Chem Phys / A smooth particle mesh Ewald method by Essmann (1995)
  24. {'journal-title': 'AMBER 4.1', 'year': '1994', 'author': 'Pearlman', 'key': '10.1016/S0959-440X(96)80046-7_BIB24'} / AMBER 4.1 by Pearlman (1994)
  25. 10.1021/ja00119a045 / J Am Chem Soc / Molecular dynamics simulations on solvated biomolecular systems: the particle mesh Ewald method leads to stable trajectories of DNA, RNA and proteins by Cheatham (1995)
  26. 10.1016/0009-2614(95)00845-U / Chem Phys Lett / Accurate crystal molecular dynamics simulations using particle-mesh-Ewald: RNA dinucleotides — ApU and GpC by Lee (1995)
  27. 10.1021/ja00122a034 / J Am Chem Soc / Toward the accurate modeling of DNA: the importance of long-range electrostatics by York (1995)
  28. 10.1063/1.468564 / J Chem Phys / Molecular dynamics simulation studies of a high resolution Z-DNA crystal by Lee (1995)
  29. 10.1021/ja00116a001 / J Am Chem Soc / Molecular dynamics of RNA with the OPLS force field. Aqueous simulation of a hairpin containing a tetranucleotide loop by Zichi (1995)
  30. 10.1016/S0006-3495(96)79298-6 / Biophys J / H-bond stability in the tRNAAsp anticodon hairpin: three nanoseconds of multiple molecular dynamics trajectories by Auffinger (1996)
  31. {'key': '10.1016/S0959-440X(96)80046-7_BIB31_1', 'article-title': 'Hydration of C-H groups in tRNA', 'volume': '103', 'author': 'Auffinger', 'year': '1996', 'journal-title': 'J Chem Soc Faraday Trans'} / J Chem Soc Faraday Trans / Hydration of C-H groups in tRNA by Auffinger (1996)
  32. 10.1002/bip.360350112 / Biopolymers / Molecular dynamics simulations of the effects of ring-saturated thymine lesions on DNA structure by Miaskiewicz (1995)
  33. 10.1080/07391102.1994.10508764 / J Biomol Struct Dyn / Molecular modelling study of DNA—Troegers bases interactions by Coppel (1994)
  34. 10.1073/pnas.91.16.7673 / Proc Natl Acad Sci USA / Relative binding affinities of distamycin and its analog to d(CGCAAGTTGGC)·d(GCCAACTTGCG): comparison of simulation results with experiment by Singh (1994)
  35. 10.1016/0076-6879(94)41074-7 / Methods Enzymol / Use of molecular dynamics and free energy perturbation calculations in anti-human immunodeficiency virus drug design by McCarrick (1994)
  36. 10.1111/j.1432-1033.1995.0555h.x / Eur J Biochem / Molecular dynamics study of the binding of elsamicin A to DNA by Alhambra (1995)
  37. 10.1006/jmbi.1994.1304 / J Mol Biol / Combined conformational search and finite-difference poisson—Boltzmann approach for flexible docking. Application to an operator mutation in the lambda repressor—operator complex by Zacharias (1994)
  38. 10.1080/07391102.1994.10508740 / J Biomol Struct Dyn / Molecular dynamics simulations in solvent of the glucocorticoid receptor protein in complex with a glucocorticoid response element DNA sequence by Harris (1994)
  39. 10.1016/S0006-3495(95)80203-1 / Biophys J / Molecular dynamics simulations of the glucocorticoid receptor DNA-binding domain in complex with DNA and free in solution by Eriksson (1995)
  40. 10.1093/nar/22.8.1444 / Nucleic Acids Res / Theoretical studies of DNA—RNA hybrid conformations by Sanghani (1994)
  41. 10.1080/07391102.1994.10508061 / J Biomol Struct Dyn / Molecular dynamics simulations of a r(GA12G)·d(CT12C) hybrid duplex by Fritsch (1994)
  42. 10.1016/0968-0896(95)00029-G / Bioorg Med Chem / Molecular mechanics and dynamics studies on two structurally related amide-modified DNA backbones for antisense technology by Fritsch (1995)
  43. 10.1021/bi00015a008 / Biochemistry / Structure and dynamics of a DNA—RNA hybrid duplex with a chiral phosphorothionate moiety: NMR and molecular dynamics with conventional and time-averaged restraints by Gonzàlez (1995)
  44. 10.1006/jmbi.1993.1593 / J Mol Biol / Molecular dynamics with weighted time-averaged restraints for a DNA octamer. Dynamic interpretation of nuclear magnetic resonance data by Schmitz (1993)
  45. 10.1002/bip.360360308 / Biopolymers / Symmetry and structure of RNA and DNA triple helices by Raghunathan (1994)
  46. 10.1080/07391102.1995.10508859 / J Biomol Struct Dyn / Structural polymorphism in d(T)12-d(A)12-d(T)12 triple helices by Kiran (1995)
  47. 10.1002/bip.360350505 / Biopolymers / Solvent effects on model d(CG-G)7 and d(TA·T)7 DNA triple helices by Cheng (1995)
  48. 10.1021/ja00113a004 / J Am Chem Soc / Nanosecond dynamics and structure of a model DNA triplex helix in saltwater solution by Weerasinghe (1995)
  49. 10.1021/bi00050a006 / Biochemistry / Structure and stability of a model pyrimidine—purine—purine DNA triple helix with a GC-T mismatch by simulation by Weerasinghe (1995)
  50. 10.1016/S0969-2126(00)00005-8 / Structure / Solution structure of a pyrimidine—purine—pyrimidine DNA triplex containing T·AT, C+·GC and G·TA Triples by Radhakrishnan (1994)
  51. 10.1006/jmbi.1994.1534 / J Mol Biol / Solution structure and hydration patterns of a pyrimidine—purine—pyrimidine DNA triplex containing a novel T·CG base-triple by Radhakrishnan (1994)
  52. 10.1002/bip.360340908 / Biopolymers / Conformational polymorphism in telomeric structures: loop orientation and interloop pairing in d(G4TnG4) by Mohanty (1994)
  53. 10.1093/nar/22.24.5447 / Nucleic Acids Res / Structural properties of the [d(G3T4G3)]2 quadruplex: evidence for sequential syn—syn deoxyguanosines by Strahan (1994)
  54. 10.1080/07391102.1995.10508798 / J Biomol Struct Dyn / Rigid-body motions of sub-units in DNA: a correlation analysis of a 200 ps molecular dynamics simulation by Briki (1995)
  55. 10.1002/bip.360330803 / Biopolymers / Conformational transitions using molecular dynamics with minimum biasing by Harvey (1993)
  56. 10.1093/nar/22.3.514 / Nucleic Acids Res / Dynamics of transfer RNAs analyzed by normal mode calculation by Nakamura (1994)
  57. {'key': '10.1016/S0959-440X(96)80046-7_BIB57', 'first-page': '25', 'article-title': 'Prediction and experimental investigation of RNA secondary and tertiary foldings', 'author': 'Westhof', 'year': '1994'} / Prediction and experimental investigation of RNA secondary and tertiary foldings by Westhof (1994)
  58. 10.1016/S1016-8478(23)17343-2 / Mol Cells / Automated modeling of the RNA folding process by Kim (1995)
  59. 10.1093/nar/23.21.4471 / Nucleic Acids Res / Alignment editing and identification of consensus secondary structures for nucleic acid sequences: interactive use of dot matrix representations by Davis (1995)
  60. 10.1093/nar/23.14.2791 / Nucleic Acids Res / Well-determined regions in RNA secondary structure prediction: analysis of small subunit ribosomal RNA by Zuker (1995)
  61. {'key': '10.1016/S0959-440X(96)80046-7_BIB61', 'first-page': '559', 'article-title': 'A comparison of thermodynamic foldings with comparatively derived structures of 16S and 16S like rRNAs', 'volume': '1', 'author': 'Konings', 'year': '1995', 'journal-title': 'RNA'} / RNA / A comparison of thermodynamic foldings with comparatively derived structures of 16S and 16S like rRNAs by Konings (1995)
  62. 10.1016/0301-4622(94)00130-C / Biophys Chem / A genetic algorithm to search for optimal and suboptimal RNA secondary structures by Benedetti (1995)
  63. 10.1006/jmbi.1995.0356 / J Mol Biol / The computer simulation of RNA folding pathways using a genetic algorithm by Gultyaev (1995)
  64. 10.1006/jmbi.1995.0608 / J Mol Biol / An interactive framework of RNA secondary structure prediction with a dynamical treatment of constraints by Gaspin (1995)
  65. 10.1002/bip.360290621 / Biopolymers / The equilibrium partition function and base pair binding probabilities for RNA secondary structure by McCaskill (1990)
  66. 10.1007/BF00192203 / Eur Biophys J / Statistics of RNA melting by Tacker (1994)
  67. 10.1039/ft9959102531 / J Chem Soc Faraday Trans / Thermodynamic properties of transfer RNA: a computational study by Higgs (1995)
  68. 10.1146/annurev.bi.64.070195.003555 / Annu Rev Biochem / Diversity of oligonucleotides functions by Gold (1995)
  69. 10.1093/nar/22.8.1368 / Nucleic Acids Res / Arrays of complementary oligonucleotides for analysing the hybridisation behaviour of nucleic acids by Southern (1994)
  70. 10.1063/1.470461 / J Phys Chem / Statistical thermodynamics of double-stranded polymer molecules by Chen (1995)
  71. 10.1209/0295-5075/25/1/009 / Europhys Lett / Complexity and tractability. Statistical mechanic of helix-coil transitions in circular DNA as a model-problem by Yeramian (1994)
  72. 10.1016/0166-1280(93)87163-8 / J Mol Struct / Modelling the three-dimensional structure of ribonucleic acids by Westhof (1993)
  73. 10.1111/j.1432-1033.1995.0365h.x / Eur J Biochem / The structure of ribosomal RNA: a three-dimensional jigsaw puzzle by Brimacombe (1995)
  74. 10.1021/bi00236a019 / Biochemistry / Predicting the three-dimensional folding of transfer tRNA with a computer modeling protocol by Hubbard (1991)
  75. 10.1126/science.1716375 / Science / The combination of symbolic and numerical computation for three-dimensional modeling of RNA by Major (1991)
  76. 10.1093/nar/23.3.419 / Nucleic Acids Res / A genetic algorithm based molecular modeling technique for RNA stem-loop structures by Ogata (1995)
  77. 10.1006/jmbi.1994.0120 / J Mol Biol / B-DNA twisting correlates with base pair morphology by Gorin (1995)
  78. 10.1080/07391102.1995.10508868 / J Biomol Struct Dyn / The construction of DNA helical duplexes along prescribed 3-D curves by Tung (1995)
  79. 10.1002/bip.360340112 / Biopolymers / Configurational statistics of the DNA duplex: extended generator matrices to treat the rotations and translations of adjacent residues by Marky (1994)
  80. 10.1002/bip.360340113 / Biopolymers / Spatial translational motions of base pairs in DNA molecules: application of the extended matrix generator method by Marky (1994)
  81. 10.1021/j100051a018 / J Phys Chem / Elasticity theory and numerical analysis of DNA supercoiling: an application to DNA looping by Westcott (1995)
  82. 10.1016/S0006-3495(95)80223-7 / Biophys J / Monte Carlo simulations of supercoiling free energies for unknotted and trefoil knotted DNAs by Gebe (1995)
  83. 10.1002/bip.360360509 / Biopolymers / Effect of anisotropy of the bending rigidity on the supercoiling free energy of small circular DNAs by Schurr (1995)
  84. 10.1016/S0006-3495(95)80161-X / Biophys J / Modulation of intramolecular interactions in superhelical DNA by curved sequences: a Monte Carlo simulation study by Klenin (1995)
  85. 10.1002/bip.360340313 / Biopolymers / Kinetics of DNA supercoiling studies by Brownian dynamics simulation by Chirico (1994)
  86. 10.1002/bip.360340502 / Biopolymers / On higher buckling transitions in supercoiled DNA by Schlick (1994)
  87. 10.1016/S0006-3495(94)80732-5 / Biophys J / The influence of salt on the structure and energetics of supercoiled DNA by Schlick (1994)
  88. 10.1006/jmbi.1996.0035 / J Mol Biol / Duplex destabilization in superhelical DNA is predicted to occur at specific transcriptional regulatory regions by Benham (1996)
  89. 10.1063/1.470250 / J Chem Phys / Elastic rod model incorporating shear and extension, generalized nonlinear Schrödinger equations, and novel closed-form solutions for supercoiled DNA by Shi (1995)
Dates
Type When
Created 23 years, 1 month ago (July 25, 2002, 6:33 a.m.)
Deposited 8 months, 3 weeks ago (Dec. 3, 2024, 11:41 a.m.)
Indexed 1 month, 2 weeks ago (July 11, 2025, 6:41 a.m.)
Issued 29 years, 2 months ago (June 1, 1996)
Published 29 years, 2 months ago (June 1, 1996)
Published Print 29 years, 2 months ago (June 1, 1996)
Funders 0

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@article{Louise_May_1996, title={Calculations of nucleic acid conformations}, volume={6}, ISSN={0959-440X}, url={http://dx.doi.org/10.1016/s0959-440x(96)80046-7}, DOI={10.1016/s0959-440x(96)80046-7}, number={3}, journal={Current Opinion in Structural Biology}, publisher={Elsevier BV}, author={Louise-May, Shirley and Auffinger, Pascal and Westhof, Eric}, year={1996}, month=jun, pages={289–298} }