The algorithm utilizes a novel sampling technique and employs the flexible combination of empirical and experimental scores.The project consists of four parts: a) optimization of secondary structure prediction, b) a Monte - Carlo search algorithm based on secondary structure elements, c) deriving empirical scoring functions from the Protein Data Bank (PDB), d) translation of experimental information into scoring functions. (meilerlab.org)
The repeats are confirmed by analysis of internal homology using the HHrepID algorithm and the helical composition by secondary structure prediction. (peerj.com)
In addition, the laboratory's decisive work on RNA provided the algorithm for RNA secondary structure (9) that today remains the basis for correlating RNA sequences with secondary structure prediction. (asbmb.org)