1.1. About the MembraneEditor
The CELLmicrocosmos MembraneEditor (CmME) is a software tool to create any kind of biomembrane to save it in pdb file format. It is part of the CELLmicrocosmos project in the Bioinformatics / Medical Informatics department at Bielefeld University.
The idea arose from the growing demand for machine-processable biomembranes and from the lack of remarkable software that produce them.
Wherefore do we need processible biomembranes?
Some possible usages:
- to observe them for educational reasons inside various viewers
- as part of virtual cells, e.g. to map them on the cell wall and/or organelles
- Scientific simulations
- to serve as an inital set-up for molecular dynamic simulations
Our first major publication on the MembraneEditor contains very detailed information on different application cases. If you use CmME in context of your publications, please cite us:
Sommer B, Dingersen D, Gamroth C, Schneider SE, Rubert S, Krüger J, Dietz, K-D: CELLmicrocosmos 2.2 MembraneEditor (2011): A Modular Interactive Shape-Based Software Approach To Solve Heterogeneous Membrane Packing Problems. J. Chem. Inf. Model. 51(5), 1165-1182.
A piece of membrane produced by this program. This shot was taken while displaying it inside the 'Molsoft ICM-Browser (c)'
Such membrane files can be created quickly and easily with this program. Basically, it takes only a few worksteps, although a lot of additional things can be done.
First you choose and obtain the molecules you want to include, consisting also of pdb-files.
Then you use them to build an abstract membrane, which is handled 3-dimensionally and follows the WYSIWYG principle. You finish your work by saving the membrane into a pdb-file.
A membrane as it gets presented in the editor. Each 3D-object represents the shape of a molecule. Here you see a lot of lipids combined into a bilayer, plus 2 embedded proteins. (Btw: This one is the template of the membrane in the picture above)
Before you ask: It was not intended to create "biologically 100% correct" membranes!
What the largest computer clusters are barely capable of, cannot be accomplished by an application that is designed to be run primarily on home or office machines!
But it is indeed possible to use simplified procedures to create acceptable results. A lot of approaches are imaginable, in various complexities.
The MembraneEditor includes a couple of approaches, realized by so called "Membrane Algorithms", which can be chosen by you. They are responsible for building the lipid layers according to your setup.
If you need your membrane for the purposes listed above, the already included algorithms should satisfy your needs.
And if not: A lot of efford has been made to create a plug-in system that allows easy implementation of new algorithms into the program. Even better: A user with the essential Java knowledge can write his own algorithms for his purposes. Several classes and interfaces provide the developer with data and operations for that purpose, making it unnecessary for her/him to know the structure of the rest of program.
Please cite us
If you use our program in context of your publication, please cite our work. Additional publications you will find at our website.
Sommer B, Dingersen D, Gamroth C, Schneider SE, Rubert S, Krüger J, Dietz, K-D: CELLmicrocosmos 2.2 MembraneEditor (2011): A Modular Interactive Shape-Based Software Approach To Solve Heterogeneous Membrane Packing Problems. J. Chem. Inf. Model. 51(5), 1165�1182.
Only a small number of persons have programmed this piece of software, but a large number of persons have contributed to this work - by critics, advices and new ideas. Thanks a lot to all of you!
In addition this software tool uses different packages, whose developers we also have to thank. Please refer to:
- Written by bjoern
- Category: Cm2help 1. Introduction
- Published: 12 September 2013
- Hits: 2785