CELLmicrocosmos.org - Cm3 CellEditor project - posters

CELLmicrocosmos 2 Posters

CELLmicrocosmos 2.1 - A Software Approach for the Visualization of three-dimensional PDB Membranes: GCB 2008: <a target='_blank' href='http://cellmicrocosmos.org/images/posters/cm2/Cm_2_1_poster_gcb2008__1_0.pdf'>[PDF]</a> <a target='_blank' href='http://www.biotec.tu-dresden.de/gcb2008/'>[Conference]</a> | GCC 2008: <a target='_blank' href='http://cellmicrocosmos.org/images/posters/cm2/Cm_2_1_poster_gcc2008__1_0.pdf'>[PDF]</a> <a target='_blank' href='http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3226176/'>[Conference]</a> | Model(l)ing 2009: <a target='_blank' href='http://cellmicrocosmos.org/images/posters/cm2/Cm_2_1_poster_model(l)ing2009__1_0.pdf'>[PDF]</a> <a target='_blank' href=''>[Conference]</a>

CELLmicrosmos 2.2 - Advancements in Modeling of three-dimensional PDB Membranes<br><a target='_blank' href='http://cellmicrocosmos.org/images/posters/cm2/Cm_2_2_poster_gcb2009__1_0low.pdf'>[PDF]</a> <a target='_blank' href='http://www.gcb2009.de'>[Conference]</a> <a target='_blank' href='http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2867130/'>[PubMed]</a>

Development towards a CELLmicrocosmos 2.2-based MD Edition<br><a target='_blank' href='http://cellmicrocosmos.org/images/posters/cm2/Cm_2_2_poster_3rdEuCheMS_2010__1_1new.pdf'>[PDF]</a> <a target='_blank' href='http://www.euchems.eu/events/euchems-chemistry-congresses.html'>[Conference]</a>

Coarse-Grained and All-Atom MD Simulations with Gromacs-based on CELLmicrocosmos 2.2 model membranes<br><a target='_blank' href='http://cellmicrocosmos.org/images/posters/cm2/Cm_2_2_poster_GCC_2010__1_1.pdf'>[PDF]</a> <a target='_blank' href='http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3083538/'>[Conference]</a> <a target='_blank' href='http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3083600/'>[PubMed]</a>

The GMX-Plugin for the CELLmicrocosmos MembraneEditor<br>GCC 2011: <a target='_blank' href='http://cellmicrocosmos.org/images/posters/cm2/Cm_2_2_GMX-Plugin_poster_GCC_2011__1_2lq.pdf'>[PDF]</a> <a target='_blank' href='http://www.jcheminf.com/supplements/4/S1'>[Conference]</a> <a target='_blank' href='http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3341190/'>[PubMed]</a> | Nanolayers 2013: <a target='_blank' href='http://cellmicrocosmos.org/images/posters/cm2/Cm_2_2_GMX-Plugin_poster_nanolayers_2013__1_0lq.pdf'>[PDF]</a> <a target='_blank' href='http://nanolayer.org'>[Conference]</a>

The Vesicle Builder - A Plugin for the CELLmicrocosmos MembraneEditor<br><a target='_blank' href='http://cellmicrocosmos.org/images/posters/cm2/Cm_2_2_VesicleBuilder_poster_VizBi_2012__1_1post.pdf'>[PDF]</a> <a target='_blank' href='http://vizbi.org/Posters/2012/C17'>[Conference]</a>

APL@Voro - revealing lipid domains with planar subdivisions<br><a target='_blank' href='http://cellmicrocosmos.org/images/posters/cm2/APL@Voro_poster_GCC_2012__1_1lq.pdf'>[PDF]</a> <a target='_blank' href='https://www.gdch.de/index.php?id=1400'>[Conference]</a> <a target='_blank' href='http://aplvoro.org'>[APL@Voro]</a>

CELLmicrocosmos 2.2.2 MembraneEditor and APL@Voro: interactively generate and analyse PDB-based membrane models<br><a target='_blank' href='http://cellmicrocosmos.org/images/posters/cm2/CmME_to_APL@Voro_MSnV2014__1_2lq.pdf'>[PDF]</a> <a target='_blank' href='http://www.rsc.org/ConferencesAndEvents/RSCConferences/FD/FD169/'>[Conference]</a> <a target='_blank' href='http://aplvoro.org'>[APL@Voro]</a> <a style='color: #dddd00' target='_parent' href='http://cellmicrocosmos.org/index.php/home/cellmicrocosmos-news/200-9-05-2014-poster-prize-at-faraday-discussion-169'>[PosterPrize]</a>

Details: Written by bjoern; Category: Cm project; Published: 24 October 2013; Hits: 25206

Cm2 MembraneEditor
project
- news
- posters
start ...
- startCm2 (SSL)
download ...
- downloadCm2 (SSL)
- membrane files
help ...
- 1. Introduction ...
  - 1.1. About the MembraneEditor
  - 1.2 Features
  - 1.3 The UI Components
  - 1.4 Requirements
- 2. The GUI ...
  - 2.1 Using the GUI
  - 2.2 Shortcuts
  - 2.3 3D Stereoscopy
- 3. Managing local PDB Files ...
  - 3.1 Setting a Database
  - 3.2 Handling your files
  - 3.3 Gaining Information
  - 3.4 Managing Models
- 4. The PDB Integration ...
  - 4.1 Search & Download
  - 4.2 Internet Configuration
- 5. Building a Membrane ...
  - 5.1 The File Menu
  - 5.2 Dealing with Molecules
  - 5.3 Aligning Molecules
  - 5.4 More about the 3D Feature
  - 5.5 3D-Settings
  - 5.6 Manage Title Section
- 6. Special Membrane Properties ...
  - 6.1. Using Microdomains
  - 6.2. Using Multilayers
- 7. Atomic Representation ...
  - 7.1. About
  - 7.2. Predefine Conformation
  - 7.3. Changing Granularity / Coarse Graining
- 8. The Lipid Bilayer ...
  - 8.1 Running a Membrane Algorithm
  - 8.2 Included Algorithms
  - 8.2.1 Linear Placing
  - 8.2.2 Random Placing
  - 8.2.3 Advanced Random Placing
  - 8.2.4 Simulated Annealing
  - 8.2.5 Distributor
  - 8.2.6 Atom Level Minimizer
  - 8.2.7 The Wanderer (Rookie)
- 9. Generating Output ...
  - 9.1 Pdb output settings - Dealing with limitation and compatibility issues
  - 9.2 Written Contents
  - 9.3 Preview your Membrane
  - 9.4 Saving the Membrane File
  - 9.5 Rebuild Membrane Model from existing pdb file
  - 9.6 Membrane Analysis with APL@Voro
- 10. Import / Manage Algorithms
- 11. More about the Editor ...
  - 11.1 Future Plans / Known Issues
  - 11.2 Cm2 Team
  - 11.3 Copyright
  - 11.4 List of external Sources and Packages
  - 11.5 History
developer ...
- Introduction
- Library and Documentation
- Creating a new Membrane Algorithm
- Overriding the Methods from the interface
- Essential Methods and Objects
- Finishing your Membrane Packing Algorithm
- Writing a good Membrane Algorithm
- Example
- Forcefield Development Hints
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