List of external Sources and Packages

Packages

This is a list of all non-standard JRE items which have been included in this application. Additional information like the license texts and third party remarks you will find in the source code package at

org.cellmicrocosmos.cm2.lib

available for download at

http://Cm2.CELLmicrocosmos.org

 

 

 

Name

Version

Type

Description

Usage

License

More Info

Infonode Docking Windows 1.6.1 Library A Window manager for a UI with multiple internal windows Manages the different windows in the main GUI GPL http://www.infonode.net
j3d-core, vecmath 1.5.2 Library 3D Graphics API for the Java Platform Displaying and picking of the 3D objects in the Membrane View GPL 2 (with CLASSPATH exception) http://www.j3d.org
j3d-core-utils 1.5.2 Library Additional libraries for j3d-core Picking and Navigation BSD (without advertising clause) http://www.j3d.org
JDOM 1.1.1 Library XML Java support Loading and saving of XML files Apache License (without acknowledgment clause) http://www.jdom.org
JFreeChart
JCommon
1.0.13
1.0.16
External Standalone Fast statistical visualization Visualization of the resulting percental lipid distributions and lipid/protein weights LGPL 2.1 (or later) http://www.jfree.org/jfreechart/
Jmol 12.0.40 Entire application as a jar-File A pdb viewer that can be used standalone or
as a browser applet
External previewing of the membrane or single molecules LGPL 2.1 (or later) http://jmol.sourceforge.net
Substance 4.0 Library A collection of Look & Feel's The L&F of the GUI BSD (without advertising clause) http://substance.dev.java.net
Tools from JDK 1.6.0_24 Library Acollection of tools for Java Compiling of java files GPL 2 (with linking exception) http://openjdk.java.net

Websites

The following websites are important for the functionality of CmME or include data used by CmME:

 

Name

Website

Usage

Publication

HIC-UP http://xray.bmc.uu.se/hicup/ Some lipid models packaged with CmME are downloaded from HIC-UP Kleywegt GJ, Jones TA (1998) Databases in protein crystallography. Acta Crystallogr., Sect. D: Biol. Crystallogr. 54, 1119-1131.
OPM http://opm.phar.umich.edu Semi-automatic protein placement of transmembrane, intrinsic and extrinsic proteins Lomize MA, Lomize AL, Pogozheva ID, Mosberg HI (2006) OPM: Orientations of Proteins in Membranes database. Bioinformatics 22, 623-625.
PDB http://www.pdb.org Resource for all actual PDB structures, direct connection via the Search and Download PDB's dialog Berman H, Westbrook J, Feng Z, Gilliland G, Bhat T, Weissig H, Shindyalov I, Bourne P (2000) The Protein Data Bank. Nucleic Acids Res. 28, 235-242.
PDB_TM http://pdbtm.enzim.hu Semi-automatic protein placement of transmembrane proteins Tusnády GE, Dosztányi Z, Simon I. (2005) PDB_TM: selection and membrane localization of transmembrane proteins in the protein data bank. Nucleic Acids Res. 33(Database issue), D275-278.

External Tools

Name

Website

Usage

Publication

xmgrace http://plasma-gate.weizmann.ac.il/Grace It can be used to visualize algorithm runtime graphs  
Gromacs http://www.gromacs.org A very mighty Molecular Dynamics package which can be run on cluster computers. The PDB Settings dialog can be used to export compatible PDB files. Hess B, Kutzner C, van der Spoel D, Lindahl E (2008): GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. J. Chem. Theory Comput. 4(3), 435–447.