A Software Package for the Analysis, Rebuilding, and Visualization of Three-dimensional Nucleic Acid Structures
Xiang-Jun Lu & Wilma K. Olson

3DNA was created in the hope that it will be useful, but without any guarantees. Nothing is perfect, and we strive to improve its functionalities. Any comments, constructive suggestions, and bug reports are welcome.

Deformation energies | Modified fiber models

As the section title implies, materials presented here are contributions from 3DNA users. Should you have any question regarding a specific topic, please contact the original author directly, or post your question in the 3DNA forum.

DNA deformation energies [Back to Top]

This work is from Marc Parisien (parisien@iro.umontreal.ca; www-lbit.iro.umontreal.ca) from the University of Montreal, Canada. The program is written in C++, for calculating deformation energies at the base-pair or dinucleotide step level.

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C++ program EnergyPDNA.C
Header file EnergyParams.h
Marc Parisien's note on the deformation energies [added May 11, 2005]

Please also see a related contribution from Dr. Thomas Gaillard. [added December 19, 2008]

Build modified fiber models [Back to Top]

This work is from Satoshi Yokojima (yokojima@adenine.ims.tsukuba.ac.jp) at the Institute of Materials Science, University of Tsukuba, Japan. It combines several programs in 3DNA to construct base-only fiber models with varying Rise. Further information is in this message.