Mathematically Complete Nucleotide and Protein Sequence Searching Using Ssearch

In this unit a protocol is described for predicting the structure of simple transmembrane a‐helical bundles. The protocol is based on a global molecular dynamics search (GMDS) of the configuration space of the helical bundle, yielding several candidate structures. The correct structure among these candidates is selected using information from silent amino acid substitutions, employing the premise that only the correct structure must (by definition) accept all of the silent amino acid substitutions. Thus, the correct structure is found by repeating the GMDS for several close homologs and selecting the structure that persists in all of the trials.