Motivation: To gain insight into how biopolymers fold as quickly as they do, it is useful to determine which structural elements limit the rate of RNA/protein folding.

Summary: We have created a new web server, FoldNucleus. Using this server, it is possible to calculate the folding nucleus for RNA molecules with known 3D structures—including pseudoknots, tRNAs, hairpins, and ribozymes—and for protein molecules with known 3D structures, as long as they are smaller than 200 amino acid residues. Researchers can determine and understand which elements of the structure limit the folding process for various types of RNAs and protein molecules. Experimental FE-values for 21 proteins can be found and compared to those determined by our method: http://bioinfo.protres.ru/resources/phi_values.htm.

Availability: http://bioinfo.protres.ru/foldnucleus/

Contact: ogalzit@vega.protres.ru