RANTS: Ranking of Transmembrane helices by Solvent accessibility
RANTS: RANking of Transmembrane helices by Solvent accessibility
Reference: Adamian L & Liang J. "Prediction of buried helices in multispan alpha helical membrane proteins". Proteins 2006; 63:1-5
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.