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Detailed study of the interactions driving the
formation of protein-protein complexes first requires a good description
of their interaction regions. Using concepts developed in computational
geometry and topology [2], we define these interaction
regions by interface surfaces [1] that are symmetric
and avoid fracture through the use of a relative distance threshold.
These concepts include:
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Voronoi diagram (whose application to protein data has been
pioneered by Richards) [3] |
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AlphaShape representation of molecules [4] |
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discrete flow on Delaunay simplices used to define pockets
[5] and reconstruct surfaces [6] |
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assessment of importance of topological features [7] |
Ciel is a software package
for generating these interface surfaces from protein structural
data. The current implementation consists of "engine"
code written in pure Java and a visualizer written in Java3D. Portions
of the software consist of a port and rewrite of the original C
version of AlphaShapes. While the software is written with the goal
of probing protein-protein interactions, it has a general input
mode for sets of balls and points, and may be useful for a number
of different applications, possibly including nanostructures.
| Ciel is robust and includes code for: |
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Delaunay triangulation in 3D for balls and points |
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AlphaShape generation |
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Topological persistence (as applied to AlphaShapes) |
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Interface surface generation |
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Currently only a binary version
of Ciel is available. The source code is scheduled to be released
first quarter 2006. |
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| 1. |
Y.A. Ban, H. Edelsbrunner, and J. Rudolph.
Interface Surfaces for Protein-Protein Complexes.
to appear in Proceedings of the 8th Annual International Conference
on Research in Computational Molecular Biology (RECOMB 2004).
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| 2. |
H. Edelsbrunner. Geometry and Topology for Mesh Generation.
Cambridge Univ. Press, England, 2001. |
| 3. |
F.M. Richards. Areas, volumes, packing and protein structures.
Ann. Rev. Biophys. Bioeng. 6 (1977), 151-176. |
| 4. |
H. Edelsbrunner and E.P. Mucke. Three-dimensional alpha shapes.
ACM Trans. Graphics. 13 (1994), 43-72. |
| 5. |
H. Edelsbrunner, M.A. Facello, and J. Liang.
On the definition and the construction of pockets in macromolecules.
Discrete Appl. Math. 88 (1998), 83-102. |
| 6. |
H. Edelsbrunner. Surface reconstruction by wrapping finite
sets in space. Discrete and Computational Geometry -- The Goodman-Pollack
Festschrift,
eds. B. Aronov, S. Basu, J. Pach, and M. Sharir, Springer-Verlag,
Berlin, 379-404. |
| 7. |
H. Edelsbrunner, D. Letscher, and A. Zomorodian.
Topological persistence and simplification.
Discrete Comput. Geom. 28 (2002), 511-533.
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