3DNA software allows for analyzing and reconstructing 3D nucleic acid structures using a standard reference frame.
3DNA is a reliable and versatile software package for analyzing and rebuilding three-dimensional nucleic acid structures. The software is grounded on a standard reference frame and employs mathematically rigorous and geometrically sensible techniques to calculate a comprehensive set of local base-pair, step, and helical parameters. Furthermore, the software enables users to reconstruct a structure based on these parameters with precise accuracy.
One of the most unique features of 3DNA is its ability to automatically classify a dinucleotide step as A-, B-, or TA-like, based on the positioning of the phosphorus atoms. Additionally, the software generates standardized base stacking diagrams, and Calladine-Drew style is provided as full atomic models with the sugar-phosphate backbone and of DNA, thanks to the rebuilding routines.
Created by Dr. Xiang-Jun Lu in Professor Wilma K. Olson's laboratory at the Department of Chemistry and Chemical Biology, Rutgers - The State University of New Jersey, 3DNA has since been worked on by Dr. Lu as an independent consultant in his spare time. The updated website offers more technical details about 3DNA, including working examples, which makes it easier for individuals interested in nucleic acid structures to understand "what's going on in that black box."
The software has benefited greatly from interactions with the Nucleic Acid Database (NDB) project led by Professor Helen Berman. Members of the Olson lab and users worldwide, including Dr. Zukang Feng at the PDB/NDB, Dr. A.R. Srinivarsan, Ms. Yurong Xin, Mr. Andrew Colasanti, Mr. Jin Tao, and Ms. Fei Xu, have contributed tremendously to making 3DNA an excellent tool to serve the scientific community.
One of the most unique features of 3DNA is its ability to automatically classify a dinucleotide step as A-, B-, or TA-like, based on the positioning of the phosphorus atoms. Additionally, the software generates standardized base stacking diagrams, and Calladine-Drew style is provided as full atomic models with the sugar-phosphate backbone and of DNA, thanks to the rebuilding routines.
Created by Dr. Xiang-Jun Lu in Professor Wilma K. Olson's laboratory at the Department of Chemistry and Chemical Biology, Rutgers - The State University of New Jersey, 3DNA has since been worked on by Dr. Lu as an independent consultant in his spare time. The updated website offers more technical details about 3DNA, including working examples, which makes it easier for individuals interested in nucleic acid structures to understand "what's going on in that black box."
The software has benefited greatly from interactions with the Nucleic Acid Database (NDB) project led by Professor Helen Berman. Members of the Olson lab and users worldwide, including Dr. Zukang Feng at the PDB/NDB, Dr. A.R. Srinivarsan, Ms. Yurong Xin, Mr. Andrew Colasanti, Mr. Jin Tao, and Ms. Fei Xu, have contributed tremendously to making 3DNA an excellent tool to serve the scientific community.
What's New
Version 1.5: N/A