ProBLM Web-server

ProBLM Introduction

(Pro)tein (B)ilayer (L)ipid (M)embrane (ProBLM) is a webserver that creates a combined protein-membrane complex when given a membrane protein (helical or beta-barrel) and bilayer lipid membrane (POPC, POPE or artificial). The artificial membrane is generated with ProNOI software (BMC Struct Biol. 2012 Dec 5;12:31) as a parallelepiped made of dummy atoms and has user specified dimensions. By using geometric features within alpha-helical and beta-barrel membrane proteins, ProBLM predict a protein's orientation and position when placed within a membrane environment. If the topology of the protein does not allow for correct orientation within the membrane, the protein is placed in the membrane without being oriented and the user is given the option to manually reorient it using sliders.

Please, cite the following paper if the use of ProBLM results in a paper:

Comput Math Methods Med. 2014;2014:838259. doi: 10.1155/2014/838259. Epub 2014 Jul 14.

ProBLM web server: protein and membrane placement and orientation package.

Kimmett T, Smith N, Witham S, Petukh M, Sarkar S, Alexov E

Membrane Info

POPC Membranes

More commonly found in exoplasm and/or the outer portions of a cell membrane. Phosphatidylcholines. The x and y dimensions of the membrane slab are given in the title with units of Angstroms (ie, POPC_100-50 has 100 Angstroms in x-direction and 50 in y-direction). Below are image previews of POPC membrane files provided by us.

   -POPC_50-50
   -POPC_75-75
   -POPC_100-50
   -POPC_100-100

POPE Membranes

More viscous than POPC membranes with a polar head group. Phosphatidylethanolamine. The x and y dimensions of the membrane slab are given in the title with units of Angstroms (ie, POPE_100-50 has 100 Angstroms in the x-direction and 50 in y-direction.) Below are image previews of POPE membrane files provided by us.

   -POPE_50-50
   -POPE_75-75
   -POPE_100-50
   -POPE_100-100

Artificial Membranes

Upon user request, the artificial membrane is generated by Protein Nano-Object Integrator software (BMC Struct Biol. 2012 Dec 5;12:31) as an atomic style parallelepiped with user's specified dimensions. This option allows for non-specific membrane environment, which may be advantageous compared with explicit membranes since it reduces the error of improperly assigned specific contacts between the protein and the lipids.