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PathRover—Rapid Sampling and Optimization of Molecular Motions


PathRover - Rapid Sampling and Optimization of Molecular Motions

Proteins are active, flexible machines that perform a range of different functions, but experimental knowledge on protein molecular motion is still limited. We recently intoduced Rosetta PathRover, a general framework for the generation, alignment and comparison of pathways between two known protein conformations using is rooted in probabilistic motion-planning techniques in robotics, allows the efficient generation of collision-free motion pathways, while considering a wide range of degrees of freedom (dofs) involved in the motion. PathRover is innovative tthe Rapidly exploring Random Trees (RRT) algorithm, a motion prediction algorithm.

The PathRover framework hanks to the following features: (1)  A general setup designed for the introduction of prior experimental data or expert intuitions into the RRT algorithm allows truncation of non-favorable branches and emphasis on relevant directions; (2) Integration into Rosetta (a leading framework for different modeling tasks) allows the use of state of the art energy function and conformational modeling; and (3) An efficient post-processing algorithm for the alignment and comparison of molecular motion pathways  (similar to string matching algorithms) allows the hybridization of suboptimal pathways segments to construct optimal pathways. The framework can therefore complement slower molecular dynamics techniques.  We used the framework to explore in detail molecular motions of domain swapping, Ion channels, and enzymes.

Links & Posters

  • Barak Raveh, Angela Enosh, O. Furman-Schueler, and Dan Halperin
    Rapid sampling of molecular motions with prior information constraints
    PLoS Computational Biology, 2009 [link] [bibtex]
  • Angela Enosh, Barak Raveh, O. Furman-Schueler, Dan Halperin, and N. Ben-Tal
    Generation, comparison and merging of pathways between protein conformations: Gating in \(K\)-channels
    Biophysical Journal, 2008 [link] [bibtex]
  • Poster: This poster received a best poster award in the Israeli Bioinformatics day 2008 [pdf]

PathRover - Rapid Sampling and Optimization of Molecular Motions


Angela Enosh
Dan Halperin
Barak Raveh

Arrangements of Geodesic Arcs on the Sphere – Additional Information
Movie page

This movie illustrates exact construction and maintenance of arrangements induced by arcs of great circles embedded on the sphere, also known as geodesic arcs, and exact computation of Voronoi diagrams on the sphere, the bisectors of which are geodesic arcs. This class of Voronoi diagrams includes the subclass of Voronoi diagrams of points and its generalization, power diagrams, also known as Laguerre Voronoi diagrams. The resulting diagrams are represented as arrangements, and can be passed as input to consecutive operations supported by the Arrangement_2 package of Cgal and its derivatives. The implementation handles well degenerate input and produces exact results.

Article PDF

The Movie
720×576, DivX, ~30M
720×576, XviD, ~125M
360×288, DivX, ~27M
360×288, XviD, ~31M

English subtitles (subrip)
Hebrew subtitles (subrip)


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  2. E. Berberich, E. Fogel, D. Halperin, K. Melhorn, and R. Wein. Sweeping and maintaining two-dimensional arrangements on surfaces: A first step. In Proc. 15th Annu. Eur. Symp. Alg., pages 645-656, 2007.
  3. E. Berberich and M. Kerber. Exact arrangements on tori and Dupin cyclides. In Proc. ACM Solid Phys. Model. Symp. 2008. To appear.
  4. H. Edelsbrunner and R. Seidel. Voronoi diagrams and arrangements. Disc. Comput. Geom., 1:25-44, 1986.
  5. D. Halperin, O. Setter, and M. Sharir. Constructing two-dimensional Voronoi diagrams via divide-and-conquer of envelopes in space, 2008. Manuscript.
  6. M. Meyerovitch. Robust, generic and efficient construction of envelopes of surfaces in three-dimensional space. In Proc. 14th Annu. Eur. Symp. Alg., pages 792-803, 2006. [project page]
  7. K. Sugihara. Laguerre Voronoi diagram on the sphere. J. for Geom. Graphics, 6(1):69-81, 2002.
  8. R. Wein, E. Fogel, B. Zukerman, and D. Halperin. Advanced programming techniques applied to Cgal’s arrangement package. Comput. Geom. Theory Appl., 38(1-2):37-63, 2007. Special issue on Cgal.

Yair Oz - Webcreator


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