LIPS: prediction of helix-lipid interfaces

LIPS (LIPid-facing Surface) is a convenient method for prediction of helix-lipid interfaces of TM helices from sequence information alone with accuracy of ~90%. LIPS is based on a canonical model of alpha helical coiled coil where the surface of each helix is partitioned into seven surface patches (faces) that could interact with lipids or other helices. More... Input: LIPS requires a multiple sequence alignment of the TM helix in Fasta format with no gaps as an input. Input sample Output: 1. LIPS outputs sets of residues that compose each of seven helical faces. These are numbered 0 ... 6. 2. LIPS outputs average scores (lipophilicity, entropy and lipophilicity*entropy) for every surface. The largest LIPS score indicates a probable high lipid exposure of the helical surface. The smallest LIPS score may indicate either a highly buried or a tightly packed helical face. You can download the CGI perl script here. Just change the extension to .pl after you have downloaded it