CITATION:

Web-server:
K Senthilkumar  D. Bhattacharya, M Bansal . An updated web-server for  analysis and generation of sequence dependent nucleic acid structures. (under preparation)

Algorithm:

Bansal,M., D. Bhattacharya, and B. Ravi. NUCGEN and NUCGEN: software for analysis and generation of sequence dependent nucleic acid structures.1995 Comput. Appl. Biosci. 11:281-287

Bhattacharya D, Bansal M. A general procedure for generation of curved DNA molecules. J Biomol Struct Dyn. 1988 Aug;6(1):93-104

Minimized structure:
Users are requested to include the citation for NAB and AMBERTOOLS13 in papers when backbone minimized structures are used.
 NAB (Nucleic-acid Builder) :

T. Macke and D.A. Case. Modeling unusual nucleic acid structures. In Molecular Modeling of Nucleic Acids, N.B. Leontes and J. SantaLucia, Jr., eds. (Washington, DC: American Chemical Society, 1998), pp. 379-393.

              This is bundled as a part of AmberTools, and the current version is 13. AmberTools (and hence, NAB) is distributed as source code under the GNU General Public License (GPL).

 AMBERTOOLS13 :
              D.A. Case, T.A. Darden, T.E. Cheatham, III, C.L. Simmerling, J. Wang, R.E. Duke, R. Luo, R.C. Walker, W. Zhang, K.M. Merz, B. Roberts, S. Hayik, A. Roitberg, G. Seabra, J. Swails, A.W. Goetz, I. Kolossv√°ry, K.F. Wong, F. Paesani, J. Vanicek, R.M. Wolf, J. Liu, X. Wu, S.R. Brozell, T. Steinbrecher, H. Gohlke, Q. Cai, X. Ye, J. Wang, M.-J. Hsieh, G. Cui, D.R. Roe, D.H. Mathews, M.G. Seetin, R. Salomon-Ferrer, C. Sagui, V. Babin, T. Luchko, S. Gusarov, A. Kovalenko, and P.A. Kollman (2012), AMBER 12, University of California, San Francisco