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Bioinformatics Vol. 16 no. 11 2000
Pages 1044-1045
© 2000 Oxford University Press

Applications Note

model.it : building three dimensional DNA models from sequence data

Kristian Vlahoviek 1 and Sándor Pongor 1

1 Protein Structure and Function Group, International Centre for Genetic Engineering and Biotechnology, Area Science Park, 34012 Trieste, Italy

Received on May 17, 2000 ; revised on July 11, 2000 ; accepted on July 19, 2000

Summary: A WWW server is described for creating 3D models of canonical or bent DNA starting from sequence data. Predicted DNA trajectory is first computed based on a choice of di- and tri-nucleotide models (M.G.Munteanu et al. , Trends Biochem. Sci. 23, 341–347, 1998); an atomic model is then constructed and optionally energy-minimized with constrained molecular dynamics. The data are presented as a standard PDB file, directly viewable on the user’s PC using any molecule manipulation program.

Availability: The model.it server is freely available at http://www.icgeb.trieste.it/dna/

Contact: kristian{at}icgeb.trieste.it; pongor{at}icgeb.trieste.it

Supplementary information: A series of help files is available at the above address.


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Home page
 Nucleic Acids ResHome page
K. Vlahovicek, L. Kajan, and S. Pongor
DNA analysis servers: plot.it, bend.it, model.it and IS
Nucleic Acids Res., July 1, 2003; 31(13): 3686 - 3687.
[Abstract] [Full Text] [PDF]


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