MOLE: A Voronoi Diagram-Based Explorer of Molecular Channels, Pores, and Tunnels. Export

@article{citeulike:1966940, 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.}, address = {National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno-Bohunice, Czech Republic.}, author = {Pet\v{r}ek, Martin and Ko\v{s}inov\'{a}, Pavl\'{\i}na and Ko\v{c}a, Jaroslav and Otyepka, Michal}, citeulike-article-id = {1966940}, citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.str.2007.10.007}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/17997961}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=17997961}, citeulike-linkout-3 = {http://www.sciencedirect.com/science/article/B6VSR-4R46KGV-8/2/b0b51ca7cbaa1dbcbc15b3c9fd7fd0cb}, day = {13}, doi = {10.1016/j.str.2007.10.007}, issn = {0969-2126}, journal = {Structure}, keywords = {caver, cavities, protein\_channels, structural\_bioinformatics}, month = {November}, number = {11}, pages = {1357--1363}, posted-at = {2007-11-23 15:17:04}, priority = {2}, title = {MOLE: A Voronoi Diagram-Based Explorer of Molecular Channels, Pores, and Tunnels.}, url = {http://dx.doi.org/10.1016/j.str.2007.10.007}, volume = {15}, year = {2007} }

TY - JOUR ID - citeulike:1966940 L3 - citeulike-article-id:1966940 N2 - 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. IS - 11 JF - Structure SN - 0969-2126 AD - National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno-Bohunice, Czech Republic. EP - 1363 TI - MOLE: A Voronoi Diagram-Based Explorer of Molecular Channels, Pores, and Tunnels. VL - 15 SP - 1357 KW - caver KW - cavities KW - protein_channels KW - structural_bioinformatics AU - Petřek, Martin AU - Košinová, Pavlína AU - Koča, Jaroslav AU - Otyepka, Michal PY - 2007/11/13/ UR - http://dx.doi.org/10.1016/j.str.2007.10.007 ER -