BIOMARKERS

Molecular Biopsy of Human Tumors

- a resource for Precision Medicine *

187 related articles for article (PubMed ID: 23072945)

  • 1. The DNA and RNA sugar-phosphate backbone emerges as the key player. An overview of quantum-chemical, structural biology and simulation studies.
    Šponer J; Mládek A; Šponer JE; Svozil D; Zgarbová M; Banáš P; Jurečka P; Otyepka M
    Phys Chem Chem Phys; 2012 Nov; 14(44):15257-77. PubMed ID: 23072945
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Benchmark quantum-chemical calculations on a complete set of rotameric families of the DNA sugar-phosphate backbone and their comparison with modern density functional theory.
    Mládek A; Krepl M; Svozil D; Cech P; Otyepka M; Banáš P; Zgarbová M; Jurečka P; Sponer J
    Phys Chem Chem Phys; 2013 May; 15(19):7295-310. PubMed ID: 23575975
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Geometrical and electronic structure variability of the sugar-phosphate backbone in nucleic acids.
    Svozil D; Sponer JE; Marchan I; Pérez A; Cheatham TE; Forti F; Luque FJ; Orozco M; Sponer J
    J Phys Chem B; 2008 Jul; 112(27):8188-97. PubMed ID: 18558755
    [TBL] [Abstract][Full Text] [Related]  

  • 4. Double sugar and phosphate backbone-constrained nucleotides: synthesis, structure, stability, and their incorporation into oligodeoxynucleotides.
    Zhou C; Plashkevych O; Chattopadhyaya J
    J Org Chem; 2009 May; 74(9):3248-65. PubMed ID: 19348480
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Trans Hoogsteen/sugar edge base pairing in RNA. Structures, energies, and stabilities from quantum chemical calculations.
    Mládek A; Sharma P; Mitra A; Bhattacharyya D; Sponer J; Sponer JE
    J Phys Chem B; 2009 Feb; 113(6):1743-55. PubMed ID: 19152254
    [TBL] [Abstract][Full Text] [Related]  

  • 6. Molecular dynamics and quantum mechanics of RNA: conformational and chemical change we can believe in.
    Ditzler MA; Otyepka M; Sponer J; Walter NG
    Acc Chem Res; 2010 Jan; 43(1):40-7. PubMed ID: 19754142
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Towards biochemically relevant QM computations on nucleic acids: controlled electronic structure geometry optimization of nucleic acid structural motifs using penalty restraint functions.
    Kruse H; Šponer J
    Phys Chem Chem Phys; 2015 Jan; 17(2):1399-410. PubMed ID: 25427983
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Sequence-dependent DNA structure: the role of the sugar-phosphate backbone.
    Packer MJ; Hunter CA
    J Mol Biol; 1998 Jul; 280(3):407-20. PubMed ID: 9665845
    [TBL] [Abstract][Full Text] [Related]  

  • 9. How to understand quantum chemical computations on DNA and RNA systems? A practical guide for non-specialists.
    Šponer J; Šponer JE; Mládek A; Banáš P; Jurečka P; Otyepka M
    Methods; 2013 Nov; 64(1):3-11. PubMed ID: 23747334
    [TBL] [Abstract][Full Text] [Related]  

  • 10. A-minor tertiary interactions in RNA kink-turns. Molecular dynamics and quantum chemical analysis.
    Réblová K; Šponer JE; Špačková N; Beššeová I; Šponer J
    J Phys Chem B; 2011 Dec; 115(47):13897-910. PubMed ID: 21999672
    [TBL] [Abstract][Full Text] [Related]  

  • 11. [The effect of electrostatic interactions on the conformation of the sugar-phosphate backbone in DNA].
    Pechenaia VI
    Mol Biol (Mosk); 1992; 26(6):1416-25. PubMed ID: 1491682
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Sugar-thioacetamide backbone in oligodeoxyribonucleosides for specific recognition of nucleic acids.
    Gogoi K; Gunjal AD; Kumar VA
    Chem Commun (Camb); 2006 Jun; (22):2373-5. PubMed ID: 16733584
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Non-Watson-Crick base pairing in RNA. quantum chemical analysis of the cis Watson-Crick/sugar edge base pair family.
    Sponer JE; Spacková N; Kulhanek P; Leszczynski J; Sponer J
    J Phys Chem A; 2005 Mar; 109(10):2292-301. PubMed ID: 16838999
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Molecular dynamics simulations of cyclohexyl modified peptide nucleic acids (PNA).
    Sharma S; Sonavane UB; Joshi RR
    J Biomol Struct Dyn; 2010 Apr; 27(5):663-76. PubMed ID: 20085383
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Noncanonical hydrogen bonding in nucleic acids. Benchmark evaluation of key base-phosphate interactions in folded RNA molecules using quantum-chemical calculations and molecular dynamics simulations.
    Zgarbová M; Jurečka P; Banáš P; Otyepka M; Sponer JE; Leontis NB; Zirbel CL; Sponer J
    J Phys Chem A; 2011 Oct; 115(41):11277-92. PubMed ID: 21910417
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Refinement of the Sugar-Phosphate Backbone Torsion Beta for AMBER Force Fields Improves the Description of Z- and B-DNA.
    Zgarbová M; Šponer J; Otyepka M; Cheatham TE; Galindo-Murillo R; Jurečka P
    J Chem Theory Comput; 2015 Dec; 11(12):5723-36. PubMed ID: 26588601
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Calculation of structural behavior of indirect NMR spin-spin couplings in the backbone of nucleic acids.
    Sychrovský V; Vokácová Z; Sponer J; Spacková N; Schneider B
    J Phys Chem B; 2006 Nov; 110(45):22894-902. PubMed ID: 17092041
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Structural and functional consequences of phosphate-arsenate substitutions in selected nucleotides: DNA, RNA, and ATP.
    Xu Y; Ma B; Nussinov R
    J Phys Chem B; 2012 Apr; 116(16):4801-11. PubMed ID: 22480264
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Vibrational Dynamics and Couplings of the Hydrated RNA Backbone: A Two-Dimensional Infrared Study.
    Bruening EM; Schauss J; Siebert T; Fingerhut BP; Elsaesser T
    J Phys Chem Lett; 2018 Feb; 9(3):583-587. PubMed ID: 29337564
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations.
    Mackerell AD; Feig M; Brooks CL
    J Comput Chem; 2004 Aug; 25(11):1400-15. PubMed ID: 15185334
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 10.