Nucleic Acid Secondary Structure Prediction  

  

Patel et al. '81

Dinshaw J. Patel, Sharon A. Kozlowski, Janet A. Rice, Luis A. Marky, Kenneth J. Breslauer, Chris Broka and Keiichi Itakura. "Structure dynamics and energetics of the d(CGCGAATTCGCG) dodecamer duplex and its selectively modified analogues in solution." Chapter 2 of Topics in Nucleic Acid Structure: Part 2, edited by Stephen Neidle, p. 81.

MIT QP620.T66 1981b. Referred to by Breslauer et al. '86.

  

Marky et al. '83

Luis A. Marky, Kenneth S. Blumenfeld, Sharon Kozlowski and Kenneth J. Breslauer. "Salt-Dependent Conformational Transitions in the Self-Complementary Deoxydodecanucleotide d(CGCAATTCGCG): Evidence for Hairpin Formation." Biopolymers 22:1247-1257, 1983.

Referred to by Breslauer et al. '86.

  

Yamamoto & Yoshikura '84

Kenji Yamamoto and Hiroshi Yoshikura. "Computer Programme Statistically Predicting Folding Structure of Nucleic Acids of Any Length: and Examples of Calculation." Japanese J. of Experimental Medicine 54(6):241-247, 1984.

  

Papanicolaou et al. '84

Catherine Papanicolaou, Manolo Gouy and Jacques Ninio. "An energy model that predicts the correct folding of both the tRNA and the 5S RNA molecules." Nucleic Acids Research 12(1):31-44, 1984.

  

Jacobson et al. '84

A. B. Jacobson, L. Good, J. Simonetti and M. Zuker. "Some simple computational methods to improve the folding of large RNAs." Nucleic Acids Research 12(1):45-52, 1984.

Referred to by Makarova et al. '92 a as their source for data on RNA loop energies.

  

Comay et al. '84

Eliahu Comay, Ruth Nussinov and Oded Comay. "An accelerated algorithm for calculating the secondary structure of single stranded RNAs." Nucleic Acids Research 12(1):53-66, 1984.

  

Hogeweg & Hesper '84

P. Hogeweg and B. Hesper. "Energy directed folding of RNA sequences." Nucleic Acids Research 12(1):67-74, 1984.

  

Shapiro et al. '84

Bruce A. Shapiro, Jacob Maizel, Lewis E. Lipkin, Kathleen Currey and Carol Whitney. "Generating non-overlapping displays of nucleic acid secondary structure." Nucleic Acids Research 12(1):75-88, 1984.

  

Martinez '84

Hugo M. Martinez. "An RNA folding rule." Nucleic Acids Research 12(1):323-334, 1984.

  

Yamamoto et al. '84

Kenji Yamamoto, Yoshihiro Kitamura and Hiroshi Yoshikura. "Computation of statistical secondary structure of nucleic acids." Nucleic Acids Research 12(1):335-346, 1984.

  

Quigley et al. '84

Gary J. Quigley, Lee Gehrke, David A. Roth and Philip E. Auron. "Computer-aided nucleic acid secondary structure modeling incorporating enzymatic digestion data." Nucleic Acids Research 12(1):347-366, 1984.

  

Wada & Suyama '86

Akiyoshi Wada and Akira Suyama. "Local stability of DNA and RNA secondary structure and its relation to biological functions." Progress in Biophysics and Molecular Biology 47:113-157, 1986.

A large and apparently very comprehensive review.

  

Gultyaev '91

A. P. Gultyaev. "The computer simulation of RNA folding involving pseudoknot formation." Nucleic Acids Research 19(9):2489-2494, 1991.