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


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


BACKGROUND
kristian@icgeb.trieste.it; pongor@icgeb.trieste.it


BACKGROUND
a series of help files is available at the above address.
Vlahovicek
K
K
Protein Structure and Function Group, International Centre for Genetic Engineering and Biotechnology, Area Science Park, 34012 Trieste, Italy. kristian@icgeb.trieste.it
Pongor
S
S
D001483:Base Sequence; D019295:Computational Biology; D004247:DNA / Q000737:chemistry* / Q000235:genetics; D018744:DNA, Plant / Q000737:chemistry / Q000235:genetics; D016208:Databases, Factual; D020407:Internet; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D011401:Promoter Regions, Genetic; D016415:Sequence Alignment / Q000706:statistics & numerical data; D012984:Software; D003313:Zea mays / Q000235:genetics
D018744:DNA, Plant; D004247:DNA