There is a growing interest in structural studies of DNA by both experimental and
computational approaches. Often, 3D-structural models of DNA are required, for instance, to …

Simulations of nucleic acids at different levels of structural details are increasingly used to
complement and interpret experiments in different fields, from biophysics to medicine and …

Abstract Web 3DNA (w3DNA) 2.0 is a significantly enhanced version of the widely used
w3DNA server for the analysis, visualization, and modeling of 3D nucleic-acid-containing …

We present a comprehensive software package, 3DNA, for the analysis, reconstruction and
visualization of three‐dimensional nucleic acid structures. Starting from a coordinate file in …

Close to 60% of protein sequences tracked in comprehensive databases can be mapped to
a known three-dimensional (3D) structure by standard sequence similarity searches …

We present a set of protocols showing how to use the 3DNA suite of programs to analyze,
rebuild and visualize three-dimensional nucleic-acid structures. The software determines a …

Last generation of force-fields are raising expectations on the quality of molecular dynamics
(MD) simulations of DNA, as well as to the belief that theoretical models can substitute …

Publisher Summary This chapter describes in detail the approach to determine DNA solution
structures, with improved accuracy, on the basis of nuclear Overhauser effect (NOE)-derived …

ABSTRACT 3D-footprint is a living database, updated and curated on a weekly basis, which
provides estimates of binding specificity for all protein–DNA complexes available at the …

It has been known for decades that DNA is extremely flexible and polymorphic, but our
knowledge of its accessible conformational space remains limited. Structural data, primarily …