title: MOLE: a Voronoi diagram-based explorer of molecular channels, pores, and tunnels.
abstract: We have developed an algorithm, "MOLE," for the rapid, fully automated location and characterization of molecular channels, tunnels, and pores. 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, cytochromes P450, potassium channels, DNA quadruplexes, ribozymes, and the 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.
authors.affiliation: National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno-Bohunice, Czech Republic.
authors.forename: Martin
authors.initials: M
authors.lastname: Petrek
authors.forename: Pavlína
authors.initials: P
authors.lastname: Kosinová
authors.forename: Jaroslav
authors.initials: J
authors.lastname: Koca
authors.forename: Michal
authors.initials: M
authors.lastname: Otyepka
mesh_terms: D000465:Algorithms; D018360:Crystallography, X-Ray; D030562:Databases, Protein; D007473:Ion Channels / Q000737:chemistry; D008958:Models, Molecular; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D012984:Software
chemical_list: D007473:Ion Channels; D011506:Proteins