3DNA is a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid-containing structures. The software is applicable not only to DNA (as the name 3DNA may imply), but also to complicated RNA structures and DNA-protein complexes. In 3DNA, structural analysis and model rebuilding are two sides of the same coin: the description of structure is rigorous and reversible, thus allowing for its exact reconstruction based on the derived parameters. 3DNA automatically detects all non-cannonical base pairs, base triplets and higher-order associations, and coaxially stacked helices; provides a comprehensive collection of fiber models of regular DNA and RNA helices; generates highly effective schematic presentations that reveal key features of nucleic-acid structures; performs undisturbed base mutations, and have facilities for the analysis of molecular dynamics simulation trajectories.
3DNA is under active development and support. In particular, any 3DNA-related questions are welcome and should be directed to the 3DNA forum — we strive to provide a prompt and concrete response to each and every question posted there.
More info · Seeing is believing · What’s new · 3DNA forum · Download
As the old saying goes, a picture is worth a thousand words. To help you have a better idea of what 3DNA is about, we’ve collected the following pictures; they serve to demonstrate selected features from 3DNA’s versatile functionality.
Schematic diagram of base-pair parameters
Influence of Slide and Roll on DNA helical conformation
Roll-introduced DNA bending
Global bending of DNA associated with selective B → A conformational transformation
Canonical fiber models of A-, B-, C- and Z-DNA
3DNA-generated view of a four-way DNA–RNA junction (1egk)
3DNA-detected pentaplets in the large ribosomal subunit (1jj2)
Nucleic-acid-containing structures generated with w3DNA
Analysis of DNA with a B-Z junction (2acj, left) and detection of hydration patterns (right)
Schematics images auto-generated via blocview
The following links point to tools that are relevant to 3DNA.
- Curves+ — an updated version of the well-known Curves program, and conforms to the standard base reference frame.
- SwS — a Solvation web Service for Nucleic Acids where 3DNA plays a role.
- 3D-DART — 3DNA-Driven DNA Analysis and Rebuilding Tool. Another web-interface to commonly used 3DNA functionality.
- 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.
- RasMol — a program for molecular graphics visualisation originally developed by Roger Sayle. Note that v2.7.x has problem in displaying base block files in Alchemy format.
- ImageMagick — a software suite to create, edit, compose, or convert bitmap images.
- NDB — Nucleic acids database.
The v2.1 release of 3DNA, currently in beta, contains many refinements of existing C programs, a complete migration from Perl scripts to Ruby, and additions of several significant new programs. All know bugs in v2.0 have been fixed. Highlights include:
- Added mutate_bases to perform in silico base mutations in nucleic-acid-containing structures (DNA, RNA, and their complexes with ligands and proteins). The program has two key and unique features: (1) the sugar-phosphate backbone conformation is untouched; (2) the base reference frame (position and orientation) is reserved, i.e., the mutated structure shares the same base-pair/step parameters as those of the native structure.
- Added
x3dna_ensemble, a Ruby script to automate the processing of an NMR structure ensemble or MD trajectories in MODEL/ENDMDL delineated PDB format. It has sub-commands analyze, extract, reorient, and block_iamge. To add: convert to transform Amber, Gromacs or CHARMM trajectories.
- Enhanced
find_pair with -c+ option for generating input to Curves+.
- Expanded
fiber with the -s option for generating single stranded structures; the -seq option for specifying base sequence directly on the command line; and the -r option for generating RNA structures (single or double stranded) of arbitrary ACGU sequences.
- Updated the ‘baselist.dat’ file to incorporate all types of NDB/PDB nucleotides as of February 15, 2015; refined
find_pair/analyze/mutate_bases etc to automatically detect and assign of modified bases.
- Renamed Atomic_a.pdb and Atomic.a.pdb etc for modified bases to account for Mac OS X filesystem case sensitivity issue; Copied all Perl scripts to a new directory
perl_scripts/.
- 3DNA now generates PDB files that are compliant with PDB format v3.x, and also has option to allow for three-letter nucleotide names, thus directly compatible with PdbViewer and HADDock. An option is provided to convert 3DNA-generated base rectangular blocks in Alchemy to the more widely accepted MDL molfile format (e.g. by PyMOL).
