Over the years, 3DNA had benefited greatly from interactions with the NDB project led by Professor Helen Berman. Zukang Feng at the PDB/NDB, A. R. Srinivarsan, Andrew Colasanti, Guofei Zheng, Mauricio Esguerra and other members of the Olson laboratory, Surjit Dixit (Wesleyan University), Pascal Auffinger (IBMC/CNRS, France), Ben Eisenbraun (SBGrid Consortium, Harvard Medical School), and numerous users have helped in making 3DNA a better tool to serve the scientific community.

The 3DNA software, its homepage and forum have been created and maintained by Xiang-Jun Lu. Unless specified explicitly otherwise, all posts at x3dna.org are written by Xiang-Jun Lu. The favicon and logo of the homepage and the forum were designed by Jessalyn Lu. The three 3DNA-related services — w3DNA, 3DNALandscapes and BPS — are supported by the Olson laboratory at Rutgers University.

The 3DNA project is supported by the NIH grant R01GM096889.