FoldNucleus: Web server for the prediction of RNA and protein folding nuclei from their 3D structures

Abstract

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 Φ values for 21 proteins can be found and compared with those determined by our method: http://bioinfo.protres.ru/resources/phi-values.htm.