Web Supplements
A series of experiments on k-point mutants of RNA with the software RNAmutants. The algorithms are described in Energy landscape of k-point mutants of an RNA molecule by P. Clote, J. Waldispuhl, B. Behzadi, J.-M. Steyaert, Bioinformatics, Vol. 21, 4140-4147, 2005.
Z-scores for Rfam : List of Z-scores of minimum free energy for all Rfam classes, using method described in the paper: "Structural RNA has lower folding energy than random RNA of the same dinucleotide frequency", by P. Clote, F. Ferre, E. Kranakis, D. Krizanc, RNA, 11(5) (2005).
Asymptotic expected number of base pairs in optimal secondary structure for random RNA using the Nussinov-Jacobson energy model , by P.Clote, E. Kranakis, D. Krizanc, L. Stacho, to appear in Bioinformatics Issue of Discrete Applied Mathematics.
Disulfide connectivity prediction using secondary structure information and diresidue frequencies , F. Ferre, P. Clote, Bioinformatics 21(10):2336-2346 (2005). See also DiANNA: a web server for disulfide connectivity prediction, F. Ferre, P. Clote, Nucleic Acids Research, Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W230-232