References

Geometry

• An extension of the Rigorous Base-unit Oriented Description of Nucleic Acid Structures.
  Tung, C-S., Soumpasis, D.M., Hummer, G., J. Biomol. Struc. & Dynam. 11, 1327(1994).
• A Rigorous Description of DNA Structure.
  Soumpasis, D.M. and Tung, C-S., J. Biomol. Struc. & Dynam. 6, 397(1988).
• Modeling DNA Backbone Structures.
  Tung, C-S., Computation of Biomolecular Structures:Achievements, Problems and Perspectives, D.M. Soumpasis and T.M. Jovin. eds. Springer-Verlag, NY 87 (1993).
• Agreement between Single Crystal X-Ray and Molecular Mechanical Sugar Ring Conformations.
  Garcia, A.E. and Krumhansl.J.A., J. Biomol. Struc. & Dynam. 5, 513(1987).
• Definitions and Nomenclature of Nucleic Acid Structure Parameters.
  Dickerson,R.E.,Bansal,M.,Calladine,C.R.,Diekmann,S.,Hunter.W.N., Kennard,O.,Lavery,R.,Nelson,H.C., Olson,W.K.,Saengar,W.,Shakked,Z., Sklenar,H., Soumpasis,D.M.,Tung,C-S., von Kitzing,E.,Wang,A.H.-C., and Zhurkin,V.B., EMBO J. 8, 1(1989)

Graphics

• RasMol: A program for fast realistic rendering of molecular structures with shadows.
  Sayle, R. and Bissell, A., In Proceedings of the 10th Eurographics UK '92 Conference, University of Edinburgh, Scotland, April 1992.
• Spherical Shading.
  Porter, Thomas K., Computer Graphics, 12, 282.(1978)
• Algorithm for Computer Control of a Digital Plotter.
  Bresenham, J.E., IBM Systems Journal, vol 4, no 1, pg 25(1965)

Misc

• Nonempirical Calculations on All the 29 Possible DNA Base Pairs.
  Hobza, P. and Sandofy, C., J. Am. Chem. Soc. 109, 1302(1987)
• A New Force Field for Molecular Mechanical Simulation of Nucleic Acids and Proteins.
  Weiner. S.J., Kollman, P.A., Case, D.A., Singh, U.C., Ghio, C., Alagona, G., Profeta,S., Jr., and Weiner, P., J Am. Chem. Soc. 106, 765(1984)
• Numerical recipes in C: The Art of Scientific Computing.
  Press, William H., Teukolsky, Saul A., Vetterling, William T, Flannery, Brian P. Cambridge University Press, New York, 1992.
• Atomic Coordinates and Molecular Conformations for DNA-DNA, RNA-RNA, and DNA-RNA Helices
  Arnott, S., Campbell-Smith, P. and Chandrasekaran, P., CRC Handbook of Biochemistry. Vol 2. CRC, Boca Raton, FL. P.411(1975)
• Gene Duplications in the Structural Evolution of Chymotrypsn
  McLachlan, A.D., J Mol Bio. (1979) 128, 49-79.

Trademarks

• The X Window System is a trademark of the Massachusetts Institute of Technology.
• XView is a trademark of Sun Microsystems, Inc.
• UNIX is a registered trademark of AT&T
• PostScript is a registered trademark of Adobe Systems, Inc.
• Open Software Foundation is a trademark of The Open Software Foundation, Inc.
• OSF is a trademark of Open Software Foundation, Inc.
• Motif is a trademark of Open Software Foundation, Inc.
• TIFF is a trademark of Aldus Corporation.

Acknowledgments

• Reinhard Klement of the Max-Planck- Institute for Biophysical Chemistry in Goettingen Germany for his help during the alpha testing.
• Kim Millman for her assistance in proof reading.
• Angel Garcia for donating bits of code.
• Marilyn Kwan for her work on the addition of unusual base pairs.
• Erik Winfree for suggestions and bits of code.
• Travis Campbell.