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@article{726935,
author = {Petřek, Martin and Košinová, Pavlína and Koča, Jaroslav and Otyepka, Michal},
article_number = {15},
keywords = {channels tunnels protein cavity},
language = {eng},
issn = {0969-2126},
journal = {Structure},
title = {MOLE: A Voronoi Diagram-based Explorer of Molecular Channels, Pores and Tunnels},
url = {http://mole.chemi.muni.cz},
volume = {15},
year = {2007}
}
TY - JOUR
ID - 726935
AU - Petřek, Martin - Košinová, Pavlína - Koča, Jaroslav - Otyepka, Michal
PY - 2007
TI - MOLE: A Voronoi Diagram-based Explorer of Molecular Channels, Pores and Tunnels
JF - Structure
VL - 15
IS - 15
SP - 1357-1363
EP - 1357-1363
SN - 09692126
KW - channels tunnels protein cavity
UR - http://mole.chemi.muni.cz
N2 - 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.
ER -
PETŘEK, Martin, Pavlína KOŠINOVÁ, Jaroslav KOČA and Michal OTYEPKA. MOLE: A Voronoi Diagram-based Explorer of Molecular Channels, Pores and Tunnels. \textit{Structure}. 2007, vol.~15, No~15, p.~1357-1363. ISSN~0969-2126.
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