title: HOLE: a program for the analysis of the pore dimensions of ion channel structural models.
abstract: A method (HOLE) that allows the analysis of the dimensions of the pore running through a structural model of an ion channel is presented. The algorithm uses a Monte Carlo simulated annealing procedure to find the best route for a sphere with variable radius to squeeze through the channel. Results can be displayed in a graphical fashion or visualized with most common molecular graphical packages. Advances include a method to analyze the anisotropy within a pore. The method can also be used to predict the conductance of channels using a simple empirically corrected ohmic model. As an example the program is applied to the cholera toxin B-subunit pentamer. The compatibility of the crystal structure and conductance data is established.
authors.affiliation: Department of Crystallography, Birkbeck College, London, England. o.smart@mail.cryst.bbk.ac.uk
authors.forename: O S
authors.initials: OS
authors.lastname: Smart
authors.forename: J G
authors.initials: JG
authors.lastname: Neduvelil
authors.forename: X
authors.initials: X
authors.lastname: Wang
authors.forename: B A
authors.initials: BA
authors.lastname: Wallace
authors.forename: M S
authors.initials: MS
authors.lastname: Sansom
mesh_terms: D000465:Algorithms; D016880:Anisotropy; D002772:Cholera Toxin / Q000737:chemistry; D003196:Computer Graphics; D003198:Computer Simulation; D004563:Electrochemistry; D007473:Ion Channels / Q000737:chemistry*; D008958:Models, Molecular; D015394:Molecular Structure; D009010:Monte Carlo Method; D012984:Software
chemical_list: D007473:Ion Channels; D002772:Cholera Toxin