Web Supplements

Supplementary data for Combinatorics of locally optimal RNA secondary structures, E. Fusy, P. Clote, J Math Biol. Mathematica computations for asymptotics: (1) asymptotics of external dangles , (2) asymptotics of UNAFOLD recursions .

Supplementary data for benchmarking tests in article "On Lattice Protein Structure Prediction Revisited", submitted by Ivan Dotu, Manuel Cebrian, Pascal Van Hentenryck, Peter Clote to IEEE Transactions on Computational Biology and Bioinformatics.

Python programs, Mathematica code, Maple session for article "Combinatorics of Canonical and Saturated Secondary Structures" by P. Clote, E. Kranakis, D. Krizanc and B. Salvy. J Bioinformatics and Computational Biology (2009).
Python programs, Mathematica code for article "Asymptotics of RNA shapes", by W.A. Lorenz, Y. Ponty and P. Clote, J Compu Biol (2008).
Mathematica code, Maple code and pdf file of supplementary proof for article "Asymptotics of RNA shapes", by W.A. Lorenz, Y. Ponty and P. Clote, J Compu Biol (2008).
Data output by the software RNAbor for the collection of SAM riboswitches retrieved from Rfam. The data includes EMBL accession number, sequence, minimum free energy (mfe) secondary structure predicted with RNAfold, number of k-neighbors for all k, Boltzmann probability of k-neighbors from the mfe structure. The software and applications are described in the article Partition function for structural neighbors of RNA with an application to riboswitch detection by Eva Freyhult, Vince Moulton and Peter Clote, Eva Freyhult; Vincent Moulton; Peter Clote, Bioinformatics. 2007 Aug 15;23(16):2054-62. Epub 2007 Jun 14.
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