The following links point to tools that are relevant to 3DNA.

• Curves+ — an updated version of the well-known Curves program, and it conforms to the standard base reference frame.
• 3D-DART — 3DNA-Driven DNA Analysis and Rebuilding Tool. Another web-interface to commonly used 3DNA functionality.
• do_x3dna — “do_x3dna has been developed for analysis of the DNA/RNA dynamics during the molecular dynamics simulations. It uses the 3DNA package to calculate several structural descriptors of DNA/RNA from the GROMACS MD trajectory. It executes 3DNA tools to calculate these descriptors and subsequently, extracts these output and saves into external output files as a function of time.”
• SwS — a Solvation web Service for Nucleic Acids where 3DNA plays a role.
• Raster3D — a set of tools for generating high-quality raster images of proteins or other molecules.
• MolScript — a program for displaying molecular 3D structures, such as proteins, in both schematic and detailed representations.
• Jmol — an open-source Java viewer for chemical structures in 3D with features for chemicals, crystals, materials, and biomolecules.
• PyMOL — a user-sponsored molecular visualization system on an open-source foundation.
• ImageMagick — a software suite to create, edit, compose, or convert bitmap images.
• NDB — Nucleic acids database.
• SBGrid — Excellent services for structural biology laboratories as well software developers.