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

K Vlahovicek·S Pongor
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Abstract

UNLABELLED: 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@icgeb.trieste.it; pongor@icgeb.trieste.it SUPPLEMENTARY INFORMATION: a series of help files is available at the above address.

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Base SequenceComputational BiologyDNADNA, PlantDatabases, FactualInternetModels, MolecularNucleic Acid ConformationPromoter Regions, GeneticSequence AlignmentSoftwareZea maysJournal Article

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K Vlahovicek, S Pongor. 2000. Model.it: building three dimensional DNA models from sequence data.. https://doi.org/10.1093/bioinformatics%2F16.11.1044

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