Sommer B, Dingersen T, Schneider S, Rubert S, Gamroth C. CELLmicrocosmos 2.2: advancements and applications in modeling of three-dimensional PDB membranes (Conference Abstract). In:  Journal of Cheminformatics. Journal of Cheminformatics. Vol 2(Suppl 1):O21. Springer Science and Business Media LLC;  2010

Björn Sommer

C Gamroth

E Lindahl

GE Tusnády

HM Berman

MA Lomize

S Rubert

S Schneider

T Dingersen

English

PubMed

Springer - Publisher Connector

ORAL PRESENTATION Open Access
CELLmicrocosmos 2.2: advancements and
applications in modeling of three-dimensional
PDB membranes
Björn Sommer1*, T Dingersen1, S Schneider2, S Rubert1, C Gamroth1
From 5th German Conference on Cheminformatics: 23. CIC-Workshop
Goslar, Germany. 8-10 November 2009
Background
Today, only a few programs support membrane compu-
tation 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 mem-
brane (bi-)layers: The MembraneEditor (CmME).
Results
The geometry-based, scalable and modular computation
concept supports fast to more complex membrane gen-
erations. CmME is based on the integration of two dif-
ferent types of PDB [1] models: Lipids are integrated
with editable percental distribution values and algo-
rithms. 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 mole-
cules 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) simula-
tion 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
Author details
1University of Bielefeld, Universitätsstraße 25, 33615 Bielefeld, Germany. 2D-
85748 Garching, Germany.
Published: 4 May 2010
References
1. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H,
Shindyalov IN, Bourne PE: The Protein Data Bank. Nucleic Acids Research
Oxford University Press, Oxford 2000, 28:235-242.
2. Tusnády GE, Dosztányi Z, Simon I: Transmembrane proteins in the Protein
Data Bank: identification and classification. Bioinformatics 2004,
20(17):2964-2972.
3. Lomize MA, Lomize AL, Pogozheva ID, Mosberg HI: OPM: Orientations of
Proteins in Membranes database. Bioinformatics 2006, 22:623-625.
4. 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.
doi:10.1186/1758-2946-2-S1-O21
Cite this article as: Sommer et al.: CELLmicrocosmos 2.2: advancements
and applications in modeling of three-dimensional PDB membranes.
Journal of Cheminformatics 2010 2(Suppl 1):O21.
1University of Bielefeld, Universitätsstraße 25, 33615 Bielefeld, Germany
Sommer et al. Journal of Cheminformatics 2010, 2(Suppl 1):O21
http://www.jcheminf.com/content/2/S1/O21
© 2010 Sommer et al; licensee BioMed Central Ltd.


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

Sommer Björn

Dingersen T

Schneider S

Rubert S

Gamroth C

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Journal of Cheminformatics

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Sommer, Björn

Dingersen, T.

Schneider, S.

Rubert, S.

Gamroth, C.

Publications at Bielefeld University

ORAL PRESENTATION Open AccessCELLmicrocosmos 2.2: advancements andapplications in modeling of three-dimensionalPDB membranesBjörn Sommer1*, T Dingersen1, S Schneider2, S Rubert1, C Gamroth1From 5th German Conference on Cheminformatics: 23. CIC-WorkshopGoslar, Germany. 8-10 November 2009BackgroundToday, only a few programs support membrane compu-tation and/or modeling in 3D. They enable the user tocreate very simple-structured membrane layers andusually assume a high level of bio-chemical/-physicalknowledge. The CELLmicrocosmos 2 project developeda tool providing a simplified workflow to create mem-brane (bi-)layers: The MembraneEditor (CmME).ResultsThe geometry-based, scalable and modular computationconcept supports fast to more complex membrane gen-erations. CmME is based on the integration of two dif-ferent types of PDB [1] models: Lipids are integratedwith editable percental distribution values and algo-rithms. Proteins are inserted and aligned into the bilayermanually or automatically, by using data from thePDB_TM [2] or OPM [3] database. Compatibility withother programs is offered by extensive PDB formatexport settings. High lipid densities are possible throughadvanced packing algorithms. Lipid distributions can bedeveloped by using the Plugin-Interface. Originally notintended to change the atomic structure of the mole-cules due performance issues, now it is also possible toaccess the atomic level for user-defined computations.Multiple membrane (bi-)layers and microdomains aresupported as well as a reengineering function providingthe re-editing of externally simulated PDB membranes.ConclusionsThe capabilities of CmME has been extended and testedto meet the requirements of different PDB visualizationprograms as well as molecular dynamics (MD) simula-tion environments like Gromacs [4]. The documentationand the Java Webstart application, requiring onlyan internet connection and Java 6, is accessible at:http://Cm2.CELLmicrocosmos.orgAuthor details1University of Bielefeld, Universitätsstraße 25, 33615 Bielefeld, Germany. 2D-85748 Garching, Germany.Published: 4 May 2010References1. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H,Shindyalov IN, Bourne PE: The Protein Data Bank. Nucleic Acids ResearchOxford University Press, Oxford 2000, 28:235-242.2. Tusnády GE, Dosztányi Z, Simon I: Transmembrane proteins in the ProteinData Bank: identification and classification. Bioinformatics 2004,20(17):2964-2972.3. Lomize MA, Lomize AL, Pogozheva ID, Mosberg HI: OPM: Orientations ofProteins in Membranes database. Bioinformatics 2006, 22:623-625.4. Lindahl E, Hess B, Spoel van der D: GROMACS 3.0: A package formolecular simulation and trajectory analysis. J Mol Mod 2001, 7:306-317.doi:10.1186/1758-2946-2-S1-O21Cite this article as: Sommer et al.: CELLmicrocosmos 2.2: advancementsand applications in modeling of three-dimensional PDB membranes.Journal of Cheminformatics 2010 2(Suppl 1):O21.1University of Bielefeld, Universitätsstraße 25, 33615 Bielefeld, GermanySommer et al. Journal of Cheminformatics 2010, 2(Suppl 1):O21http://www.jcheminf.com/content/2/S1/O21© 2010 Sommer et al; licensee BioMed Central Ltd.

3.0: A package for molecular simulation and trajectory analysis.

I: Transmembrane proteins in the Protein Data Bank: identification and classification. Bioinformatics

PE: The Protein Data Bank. Nucleic Acids Research Oxford

CELLmicrocosmos 2.2: advancements and applications in modeling of three-dimensional PDB membranes (Conference Abstract)

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

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