Subject: Re: CCL:tRNA modelling

From: [email-masked] (Christoph Schneider)
Date: Thu, 30 Oct 1997 09:00:32 +0100 (MET)

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: [email-masked]
> Cambridge MA, 02139-3180   or      [email-masked]
> 
> 
@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}   } 

@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}   } 

@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}   } 

@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}   } 

@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}   } 

@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                       [email-masked]       
 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