Inverse Folding of Biopolymers

This project investigates how the conventional "structure prediction problem" of biopolymers can be inverted: A target structure is selected. The question is then: Which sequences form the given target structure under predefined conditions ?
Before the inverse folding problem can be dealt with we have to define the term structure more precisely. For higher resolution the numbers of sequences which form the same structure decreases. Inverse folding is of particular interest in molecular biotechnology, where molecules with predefined structures and properties are designed. Previous work in our group resulted in algorithms for the inverse folding of RNA secondary structures.
The aim of the current project is to expand this heuristic to a systematic algorithm that can cope with more general classes of biopolymer structures. For instance we are working on inverse folding of three dimensional RNA structures. Similar approaches can be used for proteins; It is possible for instance, to apply the folding heuristics designed for RNA secondary structures also to lattice proteins.