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J Mol Graph. 1996 Dec;14(6):354-60, 376.

HOLE: a program for the analysis of the pore dimensions of ion channel structural models.

Author information

1
Department of Crystallography, Birkbeck College, London, England. o.smart@mail.cryst.bbk.ac.uk

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.

PMID:
9195488
[Indexed for MEDLINE]

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