Publication details

Multicriteria tunnel computation

Authors

MEDEK Petr BENEŠ Petr SOCHOR Jiří

Year of publication 2008
Type Article in Proceedings
Conference CGIM '08 Proceedings of the Tenth IASTED International Conference on Computer Graphics and Imaging
MU Faculty or unit

Faculty of Informatics

Citation
Field Computer hardware and software
Keywords protein; tunnel; multicriteria computation; computational geometry
Description Recent approaches to tunnel computation in protein molecules based on computational geometry are able to satisfactorily compute the narrowest possible width of any tunnel leading from a specified position inside the protein molecule to its surface. However, chemists are not only interested in the minimal width of a tunnel, they would also like to consider other criteria such as the length of the tunnel or its volume. In this paper we present an extension of the recent approach to tunnel computation which could take these other criteria into account. Using Delaunay triangulation we compute the set of all the tunnels which have the widest possible narrowest part, and select the best representative of this set in view of its additional criteria. Even though the extension is straightforward, it has many useful practical impacts. The major contribution of this approach is that it allows us to evaluate dynamic properties of protein molecules by tracing a computed tunnel in the sequence of several molecule snapshots in time. This new approach was implemented and piloted on real biochemical data.
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