Mathews Lab Publications

Additional Information for:

Tyagi, R., & Mathews, D.H. (2007). Predicting Helical Coaxial Stacking in RNA Multibranch Loops. RNA. 13: 939 - 951.

A table, in Microsoft Excel format, that provides the list of the coaxial stacks that are predicted by free energy minimization and the coaxial stacks that are found in the crystal structures (listed in Table 1). The stacks are classified as True Positives (the stacks that are predicted by free energy minimization and are found to exist in the corresponding crystal structure), False Positives (the stacks that are predicted by free energy minimization and are not found to exist in the corresponding crystal structure) and False Negatives (the stacks that are not predicted by free energy minimization but are found to exist in the corresponding crystal structure). The calculated probabilities of the stacks are also listed. The two terminal basepairs of the stacking helices are listed, i.e. the basepairs whose coordinates are used to determine the existence of stacking. The base numbers are as given in the protein data bank structure file (pdb file) of the corresponding molecule.

This file was updated on 10/21/08 to fix the entry for predictions of the D. radiodurans LSU rRNA.

Erratum:

On page 947, the reference to the find_pair utility of 3DNA should have been to:

Lu, X., & Olson, W.K. (2003). 3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. Nucleic Acids Research. 31: 5108-5121.

The 3DNA package homepage is located here.

Additional Information for: Tyagi, R., & Mathews, D.H. (2007). Predicting Helical Coaxial Stacking in RNA Multibranch Loops. RNA. 13: 939 - 951. Tyagi_Mathews.xls A table, in Microsoft Excel format, that provides the list of the coaxial stacks that are predicted by free energy minimization and the coaxial stacks that are found in the crystal structures (listed in Table 1). The stacks are classified as True Positives (the stacks that are predicted by free energy minimization and are found to exist in the corresponding crystal structure), False Positives (the stacks that are predicted by free energy minimization and are not found to exist in the corresponding crystal structure) and False Negatives (the stacks that are not predicted by free energy minimization but are found to exist in the corresponding crystal structure). The calculated probabilities of the stacks are also listed. The two terminal basepairs of the stacking helices are listed, i.e. the basepairs whose coordinates are used to determine the existence of stacking. The base numbers are as given in the protein data bank structure file (pdb file) of the corresponding molecule. This file was updated on 10/21/08 to fix the entry for predictions of the D. radiodurans LSU rRNA. Erratum: On page 947, the reference to the find_pair utility of 3DNA should have been to: Lu, X., & Olson, W.K. (2003). 3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. Nucleic Acids Research. 31: 5108-5121. The 3DNA package homepage is located here.