Links to other useful software
A quick Google search finds many outside links to the 3DNA home page. The list given below points to some of the resources that we have found most useful in our own work.
- Nucleic Acid Database (and PDB), where base-pair parameters and the schematic base block images are generated with 3DNA
- Curves, a well-known program, with unique features for analyzing nucleic acid structures
- RasMol, an easy-to-use, very popular molecular display program
- MolScript, a useful program for creating schematic or detailed molecular graphics images, especially for proteins
- Raster3D, a program that generates photo realistic molecular graphic images
- The RNA World Website at IMB Jena, where there is a repository of nucleic acid structures
- nuccyl, a
Perl program that allows PyMOL
to display atomic models of nucleic acids in a highly simplified
representation. Please note that find_pair can
find all possible base pairs in a given nucleic acid structure, not
just for DNA. Please refer to "User's Manual" and
"FAQ" sections for further technical
details. As a matter of fact, the RNAView program is based on an
earlier version of find_pair for locating base pairs. Note
also that the Raster3D input files created by various 3DNA programs
(such as stack2img, r3d_atom, blocview) can also
be fed
directly into PyMol for generating high-quality ray-traced images.
See also my blog posts: "Does 3DNA work for RNA?" and "blocview: a simple, effective visualization tool for nucleic acid structures". - From 3D structure to 1D base sequence and the analysis of microarray experiments: I am currently working on bioinformatics!