SIDD Theory

User Manual and References

SIDD stands for Stress-Induced (DNA) Duplex Destabilization

Information for users:

• User Manual for WebSIDD [PDF]

• SIDD model for nearest neighbor energetics [PDF]

• WebSIDD Application Note [PDF]

• Detailed description of SIDD model [PDF File]

• SIDD applications [Example 1] [Example 2]
  

More papers related to development of SIDD theory and models:

Craig J. Benham, 1990. Theoretical analysis of heteropolymeric transitions 
in superhelical DNA molecules of specified sequence. J. Chem. Phys. 
92:6294-6305.

Craig J. Benham, 1992. Energetics of the strand separation transition in 
superhelical DNA. J. Mol. Biol. 225:835-847.

Hongzhi Sun, Mihaly Mezei, Richard M. Fye and Craig J. Benham, 1995. 
Monte Carlo analysis of conformational transitions in superhelical DNA. 
J. Chem. Phys. 103:8653-8665. 

Richard M. Fye and Craig J. Benham, 1999. Exact method for numerically
analyzing a model of local denaturation in superhelically stressed DNA.
Physical Review E 59:2408-3426. 

Advanced WebSIDD program

---

Last modified by C. Bi on January 5, 2003