Funded by




This subproject aims at developing interactive methods for visualization and analysis of dynamic protein-solvent complexes. During the first funding period (2007-2010), basic visualizations for large dynamic molecular data were developed. However, bio-molecules often exhibit complex properties which cannot not be derived from classic molecular models. The extraction and visual representation of these properties is one of the key-points of further developments. Besides classic techniques like particle or volume rendering, the use of illustrative techniques will be extended for the visualization of dynamic structures. Another integral part is the visualization of the solvent. Here, both methods for abstracted visualizations and filtering, as well as the extraction of specific properties of the solvent and their visualization will be investigated. Furthermore, the possibilities for user interaction will be extended. Here, both the computations necessary for the visualization and the analysis have to be acomplished in real time. This is necessary to enable the user to change input parameters during the analysis with immediate visual feedback. This exploratory analysis enables the user to look for unexpected and unknown phenomena within the data.

Related work

The stage of development of available programs for the visualization of bio-molecules has not changed much during the previous funding period. The most common freely available tools for molecular visualization still include Visual Molecular Dynamics (VMD) [HDS96], PyMOL [DeL02] and UCSF Chimera [PGH+04]. The interactive visualization of long trajectories of protein-solvent-systems remains challenging, despite the constant development of these tools. Furthermore, the aforementioned tools cannot always fulfill the individual needs of the project partners within SFB, since they aim at general application scenarios for a large community of users. Especially the visualization of complicated models for proteins, like the Molecular Skin Surface [Ede99, CLM08] are, even with state-of-the-art hardware, not available without pre-computations or they cannot maintain interactive frame rates. This issue becomes even more relevant when considering the constantly increasing size of data within the context of SFB. Abstract visual representations, like the representation of molecular surface as proposed by Cipriano and Gleicher [CG07] often require heavy pre-computations and are, hence, not suitable for interactive visualization as pursued in this project. Tarini et. al [TCM06] succesfully applied different techniques to depict the spatial structure, like depth-dependend silhouettes or Ambient Occlusion to simple static molecular models (Stick and Spacefilling). However, an extension to complex molecular models and fast computation for dynamic data could still not be achieved.

None of the aforementioned programs applie special techniques to solvent molecules. Instead solvent molecules are either rendered using regular visualizations for molecules or completely omited in the rendering.


[CG07] G. Cipriano and M. Gleicher. Molecular Surface Abstraction. IEEE Trans. Vis. Comp. Graph., 13(6):1608-1615, 2007.

[CLM08] M. Chavent, B. Lévy, and B. Maigret. MetaMol: High quality visualization of Molecular Skin Surface. J. Mol. Graph. Mod., 27(2):209-216, 2008.

[DeL02] W. L. DeLano. The PyMOL Molecular Graphics System. DeLano Scientific, 2002.

[Ede99] H. Edelsbrunner. Deformable smooth surface design. Discrete & Computational Geometry, 21(1):87-115, 1999.

[HDS96] W. Humphrey, A. Dalke, and K. Schulten. VMD - Visual Molecular Dynamics. J. Mol. Graph., 14:33-38, 1996.

[PGH+04] E. F. Pettersen, T. D. Goddard, C. C. Huang, G. S. Couch, D. M. Greenblatt, E. C. Meng, and T. E. Ferrin. UCSF Chimera - A Visualization System for Exploratory Research and Analysis. J. Comp. Chem., 25(13):16051612, Oct 2004.

[TCM06] M. Tarini, P. Cignoni, and C. Montani. Ambient Occlusion and Edge Cueing for Enhancing Real Time Molecular Visualization. IEEE Trans. Vis. Comp. Graph., 12(5):1237-1244, 2006.