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 with the -t and -p options 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.
• From 3D structure to 1D base sequence and the analysis of microarray experiments: I am currently working on bioinformatics!