Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. I. Research design and results on d(CpG) steps.

@article{Beveridge2004MolecularDS,
  title={Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. I. Research design and results on d(CpG) steps.},
  author={David L. Beveridge and Gabriela Barreiro and Keunduk Byun and David A Case and Thomas E. Cheatham and Surjit B. Dixit and Elisabetta Giudice and Filip Lanka{\vs} and Richard Lavery and John H Maddocks and Roman Osman and Eleanore Seibert and Heinz Sklenar and Gautier Stoll and Kelly M. Thayer and P{\'e}ter V{\'a}rnai and Matthew A. Young},
  journal={Biophysical journal},
  year={2004},
  volume={87 6},
  pages={
          3799-813
        }
}
We describe herein a computationally intensive project aimed at carrying out molecular dynamics (MD) simulations including water and counterions on B-DNA oligomers containing all 136 unique tetranucleotide base sequences. This initiative was undertaken by an international collaborative effort involving nine research groups, the "Ascona B-DNA Consortium" (ABC). Calculations were carried out on the 136 cases imbedded in 39 DNA oligomers with repeating tetranucleotide sequences, capped on both… CONTINUE READING

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References

Publications referenced by this paper.
SHOWING 1-10 OF 80 REFERENCES

AMBER: Version 6

D. A. Case, D. A. Pearlman, +8 authors others.
  • Version 6.0. San Francisco: University of California.
  • 1999
VIEW 10 EXCERPTS
HIGHLY INFLUENTIAL

A smooth particle mesh Ewald method

VIEW 4 EXCERPTS
HIGHLY INFLUENTIAL

Curves 5.1: Helical Analysis of Irregular Nucleic Acids

R. Lavery, H. Sklenar
  • Institut de Biologie Physico-Chimique,
  • 1996
VIEW 3 EXCERPTS
HIGHLY INFLUENTIAL

Ion motions in molecular dynamics simulations on DNA.

  • Proceedings of the National Academy of Sciences of the United States of America
  • 2004
VIEW 2 EXCERPTS