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CELLmicrocosmos 2.2: advancements and applications in modeling of three-dimensional PDB membranes

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Background

Today, only a few programs support membrane computation and/or modeling in 3D. They enable the user to create very simple-structured membrane layers and usually assume a high level of bio-chemical/-physical knowledge. The CELLmicrocosmos 2 project developed a tool providing a simplified workflow to create membrane (bi-)layers: The MembraneEditor (CmME).

Results

The geometry-based, scalable and modular computation concept supports fast to more complex membrane generations. CmME is based on the integration of two different types of PDB [1] models: Lipids are integrated with editable percental distribution values and algorithms. Proteins are inserted and aligned into the bilayer manually or automatically, by using data from the PDB_TM [2] or OPM [3] database. Compatibility with other programs is offered by extensive PDB format export settings. High lipid densities are possible through advanced packing algorithms. Lipid distributions can be developed by using the Plugin-Interface. Originally not intended to change the atomic structure of the molecules due performance issues, now it is also possible to access the atomic level for user-defined computations. Multiple membrane (bi-)layers and microdomains are supported as well as a reengineering function providing the re-editing of externally simulated PDB membranes.

Conclusions

The capabilities of CmME has been extended and tested to meet the requirements of different PDB visualization programs as well as molecular dynamics (MD) simulation environments like Gromacs [4]. The documentation and the Java Webstart application, requiring only an internet connection and Java 6, is accessible at: http://Cm2.CELLmicrocosmos.org

References

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    Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE: The Protein Data Bank. Nucleic Acids Research. 2000, Oxford University Press, Oxford, 28: 235-242. 10.1093/nar/28.1.235.

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    Tusnády GE, Dosztányi Z, Simon I: Transmembrane proteins in the Protein Data Bank: identification and classification. Bioinformatics. 2004, 20 (17): 2964-2972. 10.1093/bioinformatics/bth340.

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    Lomize MA, Lomize AL, Pogozheva ID, Mosberg HI: OPM: Orientations of Proteins in Membranes database. Bioinformatics. 2006, 22: 623-625. 10.1093/bioinformatics/btk023.

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    Lindahl E, Hess B, Spoel van der D: GROMACS 3.0: A package for molecular simulation and trajectory analysis. J Mol Mod. 2001, 7: 306-317.

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Author information

Correspondence to Björn Sommer.

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Keywords

  • Packing Algorithm
  • Membrane Layer
  • Complex Membrane
  • Physical Knowledge
  • Advanced Packing