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