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

J Mol Graph. 1996 Dec;14(6):354-60, 376. doi: 10.1016/s0263-7855(97)00009-x.


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Anisotropy
  • Cholera Toxin / chemistry
  • Computer Graphics
  • Computer Simulation
  • Electrochemistry
  • Ion Channels / chemistry*
  • Models, Molecular*
  • Molecular Structure
  • Monte Carlo Method
  • Software*


  • Ion Channels
  • Cholera Toxin