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

Abstract

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.