BALLView: An object-oriented molecular visualization and modeling framework
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We present BALLView, an extensible tool for visualizing and modeling bio-molecular structures. It provides a variety of different models for bio-molecular visualization, e.g. ball-and-stick models, molecular surfaces, or ribbon models. In contrast to most existing visualization tools, BALLView also offers rich functionality for molecular modeling and simulation, including molecular mechanics methods (AMBER and CHARMM force fields), continuum electrostatics methods employing a Finite-Difference Poisson Boltzmann solver, and secondary structure calculation. Results of these computations can be exported as publication quality images or as movies. Even unexperienced users have direct access to this functionality through an intuitive graphical user interface, which makes BALLView particularly useful for teaching. For more advanced users, BALLView is extensible in different ways. Owing to its framework design, extension on the level of C‰+‰‰+ code is very convenient. In addition, an interface to the scripting language Python allows the interactive rapid prototyping of new methods. BALLView is portable and runs on all major platforms (Windows, MacOS X, Linux, most Unix flavors). It is available free of charge under the GNU Public License (GPL) from our website http://www.ballview.org.
KeywordsMolecular dynamics Molecular mechanics Molecular modeling Rapid prototyping Molecular visualization
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This work was supported in parts by Deutsche Forschungsgemeinschaft grants BIZ 1/1-3, BIZ 4/1-1 and LE 952/2-3. We want to thank the following student workers and fellow team members for their efforts: Andreas Bertsch, Andreas Kerzmann, Anne Dehof, Bettina Leonhardt, Carla Haid, Christian Bender.
- 2.DeLano W.L. The PyMOL molecular graphics system, 2002.Google Scholar
- 3.Discovery Studio (2005): http://www.accelrys.com/products/dstudio/index.html.Google Scholar
- 6.AVS visualization software (2005): http://www.avs.com.Google Scholar
- 7.Open MOIV: http://www.tecn.upf.es/openmoiv/.Google Scholar
- 8.Open Inventor: http://oss.sgi.com/projects/inventor/.Google Scholar
- 9.SYBYL 7.0, Tripos Inc., 1699 South Hanley Rd., St. Louis, Missouri, 63144, USA.Google Scholar
- 10.Molecular Operating Environment (MOE) (2005): http://www.chemcomp.com/.Google Scholar
- 12.Python scripting language (2005): http://www.python.org.Google Scholar
- 13.QT library (2005): http://www.trolltech.com.Google Scholar
- 14.14. Nicholls A., Sharp K., Honig B. (1991) Protein folding and association: Insights from the interfacial and thermodynamic properties of hydrocarbons. PROTEINS, Struct. Func. Genet. 11(4):281ffGoogle Scholar
- 16.Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N. and Bourne, P.E. The Protein Data Bank. Nucl.Acids Res., 28, (2000) 235–242.Google Scholar
- 17.MOPAC (2005): http://www.cachesoftware.com/mopac/index.shtml.Google Scholar
- 18.POVRay renderer (2005): http://www.povray.org.Google Scholar
- 24.Boghossian, N.P., Kohlbacher, O. and Lenhof, H.-P. BALL: Biochemical Algorithms Library. In Algorithm Engineering, 3rd International Workshop, WAE’99, Proceedings, volume 1668 of Lecture Notes in Computer Science (LNCS), pages 330–344. Springer, Heidelberg, 1999.Google Scholar
- 25.OpenGL library (2005): http://www.opengl.org.Google Scholar
- 26.SIP (Python bindings generator) (2005): http://www.riverbankcomputing.co.uk/sipGoogle Scholar