Contributed Lecture
Memdock: Membrane Proteins Docking Algorithm

A wide range of fundamental biological processes are mediated by membrane proteins. Despite their large number and importance, less than 1% of all 3D protein structures deposited in the PDB are of membrane proteins. This is mainly due to the challenges of crystallizing such proteins or performing NMR analyses. All the more so, there is only small number of membrane protein-protein complexes with known structure. Therefore, developing computational tools for docking membrane proteins is crucial. Numerous methods for docking globular proteins exist, however very few have been developed especially for membrane proteins and designed to address docking within the lipid bilayer environment.

We present a novel algorithm, Memdock, for docking alpha-helical membrane proteins which takes into consideration the lipid bilayer environment for docking as well as for refining and ranking the docking candidates. We show that our algorithm improves both the docking accuracy and the candidates ranking compared to algorithms which were originally designed for globular proteins.