J 2007

MOLE: A Voronoi Diagram-based Explorer of Molecular Channels, Pores and Tunnels

PETŘEK, Martin, Pavlína KOŠINOVÁ, Jaroslav KOČA and Michal OTYEPKA

Basic information

Original name

MOLE: A Voronoi Diagram-based Explorer of Molecular Channels, Pores and Tunnels

Name in Czech

MOLE: Program pro analýzu molekulových tunelů

Authors

PETŘEK, Martin (203 Czech Republic), Pavlína KOŠINOVÁ (203 Czech Republic), Jaroslav KOČA (203 Czech Republic, guarantor) and Michal OTYEPKA (203 Czech Republic)

Edition

Structure, 2007, 0969-2126

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10610 Biophysics

Country of publisher

United Kingdom of Great Britain and Northern Ireland

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

Impact factor

Impact factor: 5.231

RIV identification code

RIV/00216224:14310/07:00022790

Organization unit

Faculty of Science

UT WoS

000251023400007

Keywords in English

channels tunnels protein cavity

Tags

Tags

International impact, Reviewed
Změněno: 4/2/2008 16:57, prof. RNDr. Jaroslav Koča, DrSc.

Abstract

ORIG CZ

V originále

We have developed a new algorithm, MOLE, for the rapid, fully automated location and characterization of molecular channels. This algorithm has been made freely available on the Internet (http://mole.chemi.muni.cz), and overcomes many of the shortcomings and limitations of the recently developed CAVER software. The core of our MOLE algorithm is a Dijkstra's path search algorithm, which is applied to a Voronoi mesh. Tests on a wide variety of biomolecular systems including gramicidine, acetylcholinesterase, potassium channels, DNA quadruplexes, ribozymes and large ribosomal subunit have demonstrated that the MOLE algorithm performs well. MOLE is thus a powerful tool for exploring large molecular channels, complex networks of channels and molecular dynamics trajectories in which analysis of a large number of snapshots is required.

In Czech

MOLE: Program pro analýzu molekulových tunelů

Links

LC06030, research and development project
Name: Biomolekulární centrum
Investor: Ministry of Education, Youth and Sports of the CR, Biomolecular centre
MSM0021622413, plan (intention)
Name: Proteiny v metabolismu a při interakci organismů s prostředím
Investor: Ministry of Education, Youth and Sports of the CR, Proteins in metabolism and interaction of organisms with the environment