139 Citations to Olson et al. standard frame paper (JMB 2001)

  1. Lavery R, Moakher M, Maddocks JH, et al. "Conformational analysis of nucleic acids revisited: Curves" NUCLEIC ACIDS RESEARCH 37 (17): 5917-5929 2009.
  2. Sadlej-Sosnowska N "Quantum chemical considerations on degeneracy of the genetic code: Anticodon-codon wobble base pairing" JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM 913: 270-276 2009.
  3. Fogolari F, Haridas H, Corazza A, et al. "Molecular models for intrastrand DNA G-quadruplexes" BMC STRUCTURAL BIOLOGY 9: 2009.
  4. Wang JB, Zuo XB, Yu P, et al. "A Method for Helical RNA Global Structure Determination in Solution Using Small-Angle X-Ray Scattering and NMR Measurements" JOURNAL OF MOLECULAR BIOLOGY 393 (3): 717-734 2009.
  5. Voityuk AA "Can Charge Transfer in DNA Significantly Be Modulated by Varying the pi Stack Conformation?" JOURNAL OF PHYSICAL CHEMISTRY B 113 (43): 14365-14368 2009.
  6. Stelzer AC, Frank AT, Bailor MH, et al. "Constructing atomic-resolution RNA structural ensembles using MD and motionally decoupled NMR RDCs" METHODS 49 (2): 167-173 2009.
  7. Ouyang DF, Zhang H, Herten DP, et al. "Flexibility of Short-Strand RNA in Aqueous Solution as Revealed by Molecular Dynamics Simulation: Are A-RNA and A'-RNA Distinct Conformational Structures?" AUSTRALIAN JOURNAL OF CHEMISTRY 62 (9): 1054-1061 2009.
  8. Li S, Cooper VR, Thonhauser T, et al. "Stacking Interactions and DNA Intercalation" JOURNAL OF PHYSICAL CHEMISTRY B 113 (32): 11166-11172 2009.
  9. Jittivadhna K, Ruenwongsa P, Panijpan B "Making Ordered DNA and Protein Structures from Computer-Printed Transparency Film Cut-Outs" BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION 37 (4): 220-226 2009.
  10. Kiliszek A, Kierzek R, Krzyzosiak WJ, et al. "Structural insights into CUG repeats containing the 'stretched U-U wobble': implications for myotonic dystrophy" NUCLEIC ACIDS RESEARCH 37 (12): 4149-4156 2009.
  11. Starikov EB, Cuniberti G, Tanaka S "Conformation Dependence of DNA Exciton Parentage" JOURNAL OF PHYSICAL CHEMISTRY B 113 (30): 10428-10435 2009.
  12. Zheng GH, Lu XJ, Olson WK "Web 3DNA-a web server for the analysis, reconstruction, and visualization of three-dimensional nucleic-acid structures" NUCLEIC ACIDS RESEARCH 37: W240-W246 2009.
  13. Mallajosyula SS, Pati SK "Conformational Tuning of Magnetic Interactions in Metal-DNA Complexes" ANGEWANDTE CHEMIE-INTERNATIONAL EDITION 48 (27): 4977-4981 2009.
  14. Loza-Mejia MA, Castillo R, Lira-Rocha A "Molecular modeling of tricyclic compounds with anilino substituents and their intercalation complexes with DNA sequences" JOURNAL OF MOLECULAR GRAPHICS & MODELLING 27 (8): 900-907 2009.
  15. Chung YS, Brendler T, Austin S, et al. "Structural insights into the cooperative binding of SeqA to a tandem GATC repeat" NUCLEIC ACIDS RESEARCH 37 (10): 3143-3152 2009.
  16. Morgado CA, Jurecka P, Svozil D, et al. "Balance of Attraction and Repulsion in Nucleic-Acid Base Stacking: CCSD(T)/Complete-Basis-Set-Limit Calcu lations on Uracil Dimer and a Comparison with the Force-Field Description" JOURNAL OF CHEMICAL THEORY AND COMPUTATION 5 (6): 1524-1544 2009.
  17. Marathe A, Karandur D, Bansal M "Small local variations in B-form DNA lead to a large variety of global geometries which can accommodate m ost DNA-binding protein motifs" BMC STRUCTURAL BIOLOGY 9: 2009.
  18. Previti C, Harari O, Zwir I, et al. "Profile analysis and prediction of tissue-specific CpG island methylation classes" BMC BIOINFORMATICS 10: 2009.
  19. Cysewski P "The post-SCF quantum chemistry characteristics of inter- and intra-strand stacking interactions in d(CpG) and d(GpC) steps found in B-DNA, A-DNA and Z-DNA crystals" JOURNAL OF MOLECULAR MODELING 15 (6): 597-606 2009.
  20. Spitzer GM, Wellenzohn B, Markt P, et al. "Hydrogen-Bonding Patterns of Minor Groove-Binder-DNA Complexes Reveal Criteria for Discovery of New Scaffolds" JOURNAL OF CHEMICAL INFORMATION AND MODELING 49 (4): 1063-1069 2009.
  21. Becker NB, Everaers R "DNA nanomechanics: How proteins deform the double helix" JOURNAL OF CHEMICAL PHYSICS 130 (13): 2009.
  22. Becker NB, Everaers R "DNA Nanomechanics in the Nucleosome" STRUCTURE 17 (4): 579-589 2009.
  23. Gil A, Branchadell V, Bertran J, et al. "An Analysis of the Different Behavior of DNA and RNA through the Study of the Mutual Relationship between Stacking and Hydrogen Bonding" JOURNAL OF PHYSICAL CHEMISTRY B 113 (14): 4907-4914 2009.
  24. Samanta S, Mukherjee S, Chakrabarti J, et al. "Structural properties of polymeric DNA from molecular dynamics simulations" JOURNAL OF CHEMICAL PHYSICS 130 (11): 2009.
  25. Mooers BHM "Crystallographic studies of DNA and RNA" METHODS 47 (3): 168-176 2009.
  26. Olson WK, Esguerra M, Xin YR, et al. "New information content in RNA base pairing deduced from quantitative analysis of high-resolution structures" METHODS 47 (3): 177-186 2009.
  27. Langreth DC, Lundqvist BI, Chakarova-Kack SD, et al. "A density functional for sparse matter" JOURNAL OF PHYSICS-CONDENSED MATTER 21 (8): 2009.
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  29. Xin YR, Olson WK "BPS: a database of RNA base-pair structures" NUCLEIC ACIDS RESEARCH 37: D83-D88 2009.
  30. Cui P, Wu J, Zhang GQ, et al. "Hole polarons in poly(G)-poly(C) and poly(A)-poly(T) DNA molecules" SCIENCE IN CHINA SERIES B-CHEMISTRY 51 (12): 1182-1186 2008.
  31. Czyznikowska Z, Zalesny R, Cysewski P "Quantum Chemical Study of the Nature of Stacking Interactions of 2-Oxo-adenine with Native B-DNA Purines" POLISH JOURNAL OF CHEMISTRY 82 (12): 2269-2279 2008.
  32. Gonzalez O, Li J "Modeling the sequence-dependent diffusion coefficients of short DNA molecules" JOURNAL OF CHEMICAL PHYSICS 129 (16): 2008.
  33. Ebert MO, Mang C, Krishnamurthy R, et al. "The Structure of a TNA-TNA Complex in Solution: NMR Study of the Octamer Duplex Derived from alpha-(L)-Th reofuranosyl-(3 '-2 ')-CGAATTCG" JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 130 (45): 15105-15115 2008.
  34. Wynveen A, Lee DJ, Kornyshev AA, et al. "Helical coherence of DNA in crystals and solution" NUCLEIC ACIDS RESEARCH 36 (17): 5540-5551 2008.
  35. Karymov MA, Chinnaraj M, Bogdanov A, et al. "Structure, Dynamics, and Branch Migration of a DNA Holliday Junction: A Single-Molecule Fluorescence and Modeling Study" BIOPHYSICAL JOURNAL 95 (9): 4372-4383 2008.
  36. Levy C, Pike K, Heyes DJ, et al. "Molecular basis of halorespiration control by CprK, a CRP-FNR type transcriptional regulator" MOLECULAR MICROBIOLOGY 70 (1): 151-167 2008.
  37. Bende A, Bogar F, Ladik J "The role of water and K+ ion in the charge transfer between PO4- groups of DNA and the lysine(+) and arginine(+) side chains of histone proteins" CHEMICAL PHYSICS LETTERS 463: 211-213 2008.
  38. Burin AL, Dickman JA, Uskov DB, et al. "Optical absorption spectra and monomer interaction in polymers: Investigation of exciton coupling in DNA hairpins" JOURNAL OF CHEMICAL PHYSICS 129 (9): 2008.
  39. Mura C, McCammon JA "Molecular dynamics of a kappa B DNA element: base flipping via cross-strand intercalative stacking in a microsecond-scale simulation" NUCLEIC ACIDS RESEARCH 36 (15): 4941-4955 2008.
  40. Lu XJ, Olson WK "3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures" NATURE PROTOCOLS 3 (7): 1213-1227 2008.
  41. Kenfack CA, Piemont E, Ben Gaied N, et al. "Time-resolved fluorescent properties of 8-vinyl-deoxyadenosine and 2-amino-deoxyribosylpurine exhibit different sensitivity to their opposite base in duplexes" JOURNAL OF PHYSICAL CHEMISTRY B 112 (32): 9736-9745 2008.
  42. Pfoh R, Laatsch H, Sheldrick GM "Crystal structure of trioxacarcin A covalently bound to DNA" NUCLEIC ACIDS RESEARCH 36 (10): 3508-3514 2008.
  43. Svozil D, Kalina J, Omelka M, et al. "DNA conformations and their sequence preferences" NUCLEIC ACIDS RESEARCH 36 (11): 3690-3706 2008.
  44. Schlegel MK, Essen LO, Meggers E "Duplex structure of a minimal nucleic acid" JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 130 (26): 8158-+ 2008.
  45. Kubar T, Woiczikowski PB, Cuniberti G, et al. "Efficient calculation of charge-transfer matrix elements for hole transfer in DNA" JOURNAL OF PHYSICAL CHEMISTRY B 112 (26): 7937-7947 2008.
  46. Cooper VR, Thonhauser T, Langreth DC "An application of the van der Waals density functional: Hydrogen bonding and stacking interactions between nucleobases" JOURNAL OF CHEMICAL PHYSICS 128 (20): 2008.
  47. Robeyns K, Herdewijn P, Van Meervelt L "Influence of the incorporation of a cyclohexenyl nucleic acid (CeNA) residue onto the sequence d(CGCGAATTCGCG)" NUCLEIC ACIDS RESEARCH 36 (5): 1407-1414 2008.
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  49. Sanianta S, Kabir M, Sanyal B, et al. "Twist-dependent stacking energy of base-pair steps in B-DNA geometry: A density functional theory approach" INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 108 (6): 1173-1180 2008.
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  51. Robeyns K, Herdewijn P, Van Meervelt L "Structure of the fully modified left-handed cyclohexene nucleic acid sequence GTGTACAC" JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 130 (6): 1979-1984 2008.
  52. Arauzo-Bravo MJ, Sarai A "Indirect readout in drug-DNA recognition: role of sequence-dependent DNA conformation" NUCLEIC ACIDS RESEARCH 36 (2): 376-386 2008.
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  58. Sarver M, Zirbel CL, Stombaugh J, et al. "FR3D: finding local and composite recurrent structural motifs in RNA 3D structures" JOURNAL OF MATHEMATICAL BIOLOGY 56: 215-252 2008.
  59. Banerjee A, Misra M, Pai D, et al. "Feature extraction using molecular planes for fuzzy relational clustering of a flexible dopamine reuptake inhibitor" JOURNAL OF CHEMICAL INFORMATION AND MODELING 47 (6): 2216-2227 2007.
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  61. Wadley LM, Keating KS, Duarte CM, et al. "Evaluating and learning from RNA pseudotorsional space: Quantitative validation of a reduced representation for RNA structure" JOURNAL OF MOLECULAR BIOLOGY 372 (4): 942-957 2007.
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  64. Tolstorukov MY, Colasanti AV, McCandlish DM, et al. "A novel roll-and-slide mechanism of DNA folding in chromatin: Implications for nucleosome positioning" JOURNAL OF MOLECULAR BIOLOGY 371 (3): 725-738 2007.
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  68. Shashel YV, Anishkin AG, Tolstorukov MY "Cross-correlations of base-pair and dimer step parameters of DNA" JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS 24 (6): 739-740 2007.
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  72. Matsumoto A, Olson WK "Predicted effects of local conformational coupling and external restraints on the torsional properties of single DNA molecules" MULTISCALE MODELING & SIMULATION 5 (4): 1227-1247 2006.
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Created and maintained by Dr. Xiang-Jun Lu. Last modified: Fri Nov 20 13:50:14 2009