MOLE: A Voronoi Diagram-based Explorer of Molecular Channels, Pores and Tunnels
| Authors | |
|---|---|
| Year of publication | 2007 |
| Type | Article in Periodical |
| Magazine / Source | Structure |
| MU Faculty or unit | |
| Citation | |
| Web | MOLE page |
| Field | Biophysics |
| Keywords | channels tunnels protein cavity |
| Description | 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. |
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