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Dynamic Molecular Surfaces - Nobert Lindow

Lupe [1]

Molecular surfaces are widely used in biochemistry and pharmaceutics to study molecular interactions. In particular, molecular surfaces are important when studying protein substrate docking. Since proteins often consist of several thousands of atoms, it is necessary to have fast algorithms for the computation and visualization of molecular surfaces. Richards was the first, who defined a smooth surface of molecules, which is now most often called solvent excluded surface (SES). Later Edelsbrunner defined a smooth surface of weighted points. This surface is also widely used for molecules, where it is known as molecular skin surface (MSS). This thesis presents existing algorithms, like the contour-buildup algorithm or the powercell algorithm, and modifies and parallelizes them for a very fast computation of the SES or MSS. Powerful tools for parallelization are OpenMP and CUDA. Another focus of this thesis is the realtime visualization of molecular surfaces. It will be investigated whether realtime visulization is possible by triangulation or GPU based raycasting. In addition to molecular surfaces also molecular properties shall be displayed by color-coding.

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