Multicriteria tunnel computation

MEDEK, Petr, Petr BENEŠ and Jiří SOCHOR. Multicriteria tunnel computation. In CGIM '08 Proceedings of the Tenth IASTED International Conference on Computer Graphics and Imaging. Innsbruck, Rakousko: ACTA Press, 2008, p. 160-164. ISBN 978-0-88986-720-8.

Basic information

Original name

Multicriteria tunnel computation

Name in Czech

Výpočet tunelů se zohledněním doplňujících kritérií

Authors

MEDEK, Petr (203 Czech Republic, guarantor, belonging to the institution), Petr BENEŠ (203 Czech Republic, belonging to the institution) and Jiří SOCHOR (203 Czech Republic, belonging to the institution)

Edition

Innsbruck, Rakousko, CGIM '08 Proceedings of the Tenth IASTED International Conference on Computer Graphics and Imaging, p. 160-164, 5 pp. 2008

Publisher

ACTA Press

---

Other information

Language

English

Type of outcome

Stať ve sborníku

Field of Study

20206 Computer hardware and architecture

Country of publisher

Austria

Confidentiality degree

není předmětem státního či obchodního tajemství

Publication form

printed version "print"

RIV identification code

RIV/00216224:14330/08:00024595

Organization unit

Faculty of Informatics

ISBN

978-0-88986-720-8

Keywords in English

protein; tunnel; multicriteria computation; computational geometry

Tags

computational geometry, multicriteria computation, PROTEIN, tunnel

Tags

International impact, Reviewed

---

Abstract

V originále

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.

In Czech

Existující přístupy k výpočtu tunelů v molekulách proteinů, které jsou založené na výpočetní geometrii jsou schopny vypočítat nejužší místo tunelu, vedoucího z aktivního místa na povrch molekuly. Chemici ale potřebují zohlednit i další parametry, jako je například délka tunelu nebo objem tunelu. V tomto článku je prezentováno rozšíření, které zohlední i další kritéria. Tunel, který splňuje i další kritéria může být vybrán jako vhodný reprezentant pro analýzu molekulové dynamiky. Metoda byla implementována a otestována na reálných sekvencích molekul proteinů.

---

Links

GA201/07/0927, research and development project	Name: Vizualizace proteinových struktur Investor: Czech Science Foundation, Visualization of protein structures
LC06008, research and development project	Name: Centrum počítačové grafiky (Acronym: CPG) Investor: Ministry of Education, Youth and Sports of the CR, Center of Computer Graphics