RANTS is a method for prediction of
buried TM helices from sequence
information alone with accuracy of 78% and Matthew's coefficient of 0.68 if number of such helices is known a priori.
We develop an empirical helix burial function f based on a few assumptions: More about helix burial function
Input: Please concatenate multiple sequence alignment files for every helix of the same chain.
MSA's for every helix should be separated by '>TM' as in input sample. Input sample contains data for multidrug efflux transporter Acrb (PDB: 1IWG). TM helices 10 and 4 are buried.
Importantly, if there are several chains in the protein as in cytochrome c oxidase (PDB: 1OCR), than only TM helices from the same chain should be compared to obtain a meaningful result.
Output: The script outputs TM helix names together with the value of the
helix burial function f for every helix.