MOLE swMATH ID: 18622 Software Authors: Petřek, M., Košinová, P., Koča, J., Otyepka, M. Description: MOLE: A Voronoi Diagram-Based Explorer of Molecular Channels, Pores, and Tunnels. 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. Homepage: http://www.sciencedirect.com/science/article/pii/S0969212607003759 Related Software: VirtualGL; Open Inventor; VizServer; MeVisLab; N4itk; dcm4che; muView; ProbExplorer; BioImageXD; TreeJuxtaposer; MySQL; DCMTK; VTK; PyMOL; ITK; OpenGL; nag Cited in: 3 Publications all top 5 Cited by 8 Authors 1 Barequet, Gill 1 Eppstein, David Arthur 1 Goodrich, Michael Truman 1 Hamann, Bernd 1 Hege, Hans-Christian 1 Linsen, Lars 1 Mamano, Nil 1 Petitjean, Michel Cited in 1 Serial 1 Mathematics and Visualization all top 5 Cited in 7 Fields 2 Biology and other natural sciences (92-XX) 1 General and overarching topics; collections (00-XX) 1 Geometry (51-XX) 1 Convex and discrete geometry (52-XX) 1 Computer science (68-XX) 1 Operations research, mathematical programming (90-XX) 1 Information and communication theory, circuits (94-XX) Citations by Year