Re: CCL:tRNA modelling



 Dear Ryszard Czerminski,
 you wrote:
 >
 > Dear All,
 >
 > I am looking for information about tRNA modelling.
 > In particular for MD simulations
 > and parametrization of rare nucleotides (pseudo-uracil
 > etc...)
 >
 > Ryszard Czerminski         phone : (617)354-3124 x 13
 > Moldyn, Inc.               fax   : (617)491-4522
 > 955 Massachusetts Avenue   e-mail: ryszard;at;moldyn.com
 > Cambridge MA, 02139-3180   or      ryszard;at;photon.com
 >
 >
 ;at;ARTICLE{auffinger96a,
 AUTHOR = {P. Auffinger; E. Westhof},
 TITLE = {H-bond stability in the tRNA(Asp) anticodon
 hairpin: 3 ns of multiple molecular dynamics simulations},
 JOURNAL = {Biophys J},
 YEAR = {1996},
 VOLUME = {71},
 PAGES = {940-954}   }
 ;at;ARTICLE{auffinger97,
 AUTHOR = {P. Auffinger; E. Westhof},
 TITLE = {RNA hydration: three nanoseconds of multiple
 molecular dynamics simulations of the solvated tRNAAsp
 anticodon hairpin},
 JOURNAL = {J. Mol. Biol.},
 YEAR = {1997},
 VOLUME = {269},
 PAGES = {326-341}   }
 ;at;ARTICLE{auffinger95,
 AUTHOR = {P. Auffinger; S. Louise-May; E. Westhof},
 TITLE = {Multiple molecular dynamics simulations of the
 anticodon loop of tRNAAsp in aqueous solution with
 counterions},
 JOURNAL = {J. Amer. Chem. Soc.},
 YEAR = {1995},
 VOLUME = {117},
 PAGES = {6720-6726}   }
 ;at;ARTICLE{auffinger96b,
 AUTHOR = {P. Auffinger; S. Louise-May; E. Westhof},
 TITLE = {Hydration of C-H groups in tRNA},
 JOURNAL = {Faraday Discuss},
 YEAR = {1996},
 VOLUME = {103},
 PAGES = {151-173}   }
 ;at;ARTICLE{auffinger96c,
 AUTHOR = {P. Auffinger; S. Louise-May; E. Westhof},
 TITLE = {Molecular dynamics simulations of the anticodon
 hairpin of tRNAAsp: Structuring effects of C-H...O hydrogen
 bonds and of long-range hydration forces},
 JOURNAL = {J. Am. Chem. Soc.},
 YEAR = {1996},
 VOLUME = {118},
 PAGES = {1181-1189}   }
 ;at;ARTICLE{louise96,
 AUTHOR = {S. Louise-May; P. Auffinger; E. Westhof},
 TITLE = {Calculations of nucleic acid conformations},
 JOURNAL = {Curr Opin Struct Biol},
 YEAR = {1996},
 VOLUME = {6},
 PAGES = {289-298}   }
 I listed some papers of Pascal, he did the most work published on tRNA
 MD. Contact me if you have further questions,
 best regards C.
 --
  Christoph Schneider                       csc;at;imb-jena.de
  Institute for Molecular Biotechnology
  Beutenbergstrasse 11, -Biocomputing-      Tel.: +49-3641-65-6205
  P.O. Box 100 813, D-07708 Jena, Germany   Fax:  +49-3641-65-6210