Introduction Features Methods and Definitions Precision Classification Comparision with experimental data Comparision with other computational methods Topology definitions Acknowledgements

Topology Definitions

The topologies of transmembrane proteins follow MPtopo (Jayasinghe S., Hristova K., and White S.H. (2001) MPtopo: A database of membrane protein topology Protein Science 10: 455–458).

Definitions of inner and outer membrane sides in OPM

Plasma membrane: IN – cytoplasmic, OUT – extracellular;

Endoplasmic reticulum, Golgi, nuclear, peroxisome, endosome, vacuole, and vesicle membranes: IN – cytoplasmic, OUT – luminal;

Inner bacterial membrane: IN – cytoplasmic, OUT – periplasmic or extracellular space;

Outer bacterial membrane: IN – periplasmic space, OUT – extracellular;

Inner mitochondrial or chloroplast membrane: IN – matrix/stroma, OUT –intermembrane space;

Outer mitochondrial or chloroplast membrane: IN – intermembrane space, OUT – cytoplasmic;

Chloroplast thylakoid membrane: IN- stromal, OUT – thylakoid space.